Binding Site Information of Target
Target General Information | Top | ||||
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Target ID | T08856 | Target Info | |||
Target Name | Matrix metalloproteinase-8 (MMP-8) | ||||
Synonyms | PMNL-CL; PMNL collagenase; Neutrophil collagenase; CLG1 | ||||
Target Type | Clinical trial Target | ||||
Gene Name | MMP8 | ||||
Biochemical Class | Peptidase | ||||
UniProt ID |
Drug Binding Sites of Target | Top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Ligand Name: Acetohydroxamic acid | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor | PDB:3DPF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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☰Loading data... Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
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Ligand Name: Batimastat | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | COMPLEX OF BB94 WITH THE CATALYTIC DOMAIN OF MATRIX METALLOPROTEINASE-8 | PDB:1MMB | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [2] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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☰Loading data... Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
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Ligand Name: 3-amino-azacyclotridecan-2-one | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | PROCARBOXYPEPTIDASE TERNARY COMPLEX | PDB:1KBC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
FMLTPGNPKW
88 ERTNLTYRIR98 NYTPQLSEAE108 VERAIKDAFE118 LWSVASPLIF128 TRISQGEADI 138 NIAFYQRDHG148 DNSPFDGPNG158 ILAHAFQPGQ168 GIGGDAHFDA178 EETWTNTSAN 188 YNLFLVAAHE198 FGHSLGLAHS208 SDPGALMYPN218 YAFRETSNYS228 LPQDDIDGIQ 238 AIYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RIN or .RIN2 or .RIN3 or :3RIN;style chemicals stick;color identity;select .A:157 or .A:158 or .A:159 or .A:160 or .A:189 or .A:217 or .A:218 or .A:219; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: METHYLAMINO-PHENYLALANYL-LEUCYL-HYDROXAMIC ACID | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | STRUCTURE OF HUMAN NEUTROPHIL COLLAGENASE REVEALS LARGE S1' SPECIFICITY POCKET | PDB:1MNC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
GPKWERTNLT
115 YRIRNYTPQL125 SEAEVERAIK135 DAFELWSVAS145 PLIFTGISQG155 EADINIAFYQ 165 RDHGDGSPFD175 GPNGILAHAF185 QPGQGIGGDA195 HFDAEETWTN205 TSANYNLFLV 215 AAHEFGHSLG225 LAHSSDPGAL235 MYPNYAFRET245 SNYSLPQDDI255 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PLH or .PLH2 or .PLH3 or :3PLH;style chemicals stick;color identity;select .A:179 or .A:180 or .A:181 or .A:182 or .A:183 or .A:184 or .A:210 or .A:215 or .A:218 or .A:219 or .A:222 or .A:228 or .A:237 or .A:238 or .A:239 or .A:240; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 3-Formyl-2-hydroxy-5-methyl-hexanoic acid hydroxyamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | PROCARBOXYPEPTIDASE TERNARY COMPLEX | PDB:1KBC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
FMLTPGNPKW
88 ERTNLTYRIR98 NYTPQLSEAE108 VERAIKDAFE118 LWSVASPLIF128 TRISQGEADI 138 NIAFYQRDHG148 DNSPFDGPNG158 ILAHAFQPGQ168 GIGGDAHFDA178 EETWTNTSAN 188 YNLFLVAAHE198 FGHSLGLAHS208 SDPGALMYPN218 YAFRETSNYS228 LPQDDIDGIQ 238 AIYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HLE or .HLE2 or .HLE3 or :3HLE;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:216 or .A:217 or .A:218 or .A:219; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 2-(Biphenyl-4-sulfonyl)-1,2,3,4-tetrahydro-isoquinoline-3-carboxylic acid | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | COMPLEX OF 2-(BIPHENYL-4-SULFONYL)-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID (D-TIC DERIVATIVE) WITH T CATALITIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) | PDB:1I76 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.20 Å | Mutation | No | [5] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BSI or .BSI2 or .BSI3 or :3BSI;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:213 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
4.017
ILE159
3.681
LEU160
2.864
ALA161
3.161
HIS162
4.194
ALA163
4.968
LEU193
3.529
VAL194
4.030
HIS197
3.320
GLU198
2.622
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ligand Name: {[(Biphenyl-4-Ylsulfonyl)amino]methanediyl}bis(Phosphonic Acid) | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115 | PDB:4QKZ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.20 Å | Mutation | No | [6] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QZK or .QZK2 or .QZK3 or :3QZK;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:213 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
4.298
ILE159
3.501
LEU160
2.550
ALA161
2.786
HIS162
3.388
ALA163
4.539
LEU193
3.627
VAL194
4.039
HIS197
3.236
GLU198
2.700
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Ligand Name: N-(3,4-dihydroxyphenyl)-4-phenylbenzenesulfonamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex MMP-8/BF471 (catechol inhibitor) | PDB:5H8X | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.30 Å | Mutation | No | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5XT or .5XT2 or .5XT3 or :35XT;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: N-(4,5-dioxocyclohexen-1-yl)-4-phenylbenzenesulfonamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex MMP-8/BF471 (catechol inhibitor) | PDB:5H8X | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.30 Å | Mutation | No | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7FY or .7FY2 or .7FY3 or :37FY;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: (1S)-1-{[(4'-Methoxy-1,1'-biphenyl-4-YL)sulfonyl]amino}-2-methylpropylphosphonic acid | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (S-enantiomer) | PDB:1ZS0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.56 Å | Mutation | No | [8] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIN or .EIN2 or .EIN3 or :3EIN;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:213 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
3.355
ILE159
3.322
LEU160
2.601
ALA161
3.269
HIS162
3.423
ALA163
4.372
LEU193
3.378
VAL194
3.756
HIS197
3.248
GLU198
2.532
HIS201
3.274
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Ligand Name: N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4h-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor | PDB:3DPE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AXB or .AXB2 or .AXB3 or :3AXB;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:193 or .A:194 or .A:197 or .A:198 or .A:207 or .A:212 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:221 or .A:222 or .A:224 or .A:226 or .A:227 or .A:228 or .A:230; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
4.710
ILE159
2.911
LEU160
2.618
ALA161
2.950
LEU193
3.278
VAL194
4.043
HIS197
3.371
GLU198
3.135
HIS207
4.087
GLY212
4.041
ALA213
3.584
LEU214
3.183
MET215
4.759
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ligand Name: N-{2-[(4'-Cyano-1,1'-biphenyl-4-YL)oxy]ethyl}-N'-hydroxy-N-methylurea | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex between MMP-8 and a N-hydroxyurea inhibitor | PDB:1ZP5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [9] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2NI or .2NI2 or .2NI3 or :32NI;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:213 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
4.527
ILE159
3.479
LEU160
3.176
ALA161
3.003
HIS162
4.042
ALA163
4.858
LEU193
3.698
VAL194
3.888
HIS197
3.420
GLU198
3.339
HIS201
3.738
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Ligand Name: (1R)-1-{[(4'-Methoxy-1,1'-biphenyl-4-YL)sulfonyl]amino}-2-methylpropylphosphonic acid | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex between MMP-8 and a phosphonate inhibitor (R-enantiomer) | PDB:1ZVX | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.87 Å | Mutation | No | [8] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FIN or .FIN2 or .FIN3 or :3FIN;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:213 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222 or .A:227; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
4.338
ILE159
3.349
LEU160
2.597
ALA161
2.938
HIS162
3.451
ALA163
4.470
LEU193
3.618
VAL194
3.913
HIS197
3.237
GLU198
2.868
HIS201
3.537
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Ligand Name: (5s)-5-(2-Amino-2-Oxoethyl)-4-Oxo-N-[(3-Oxo-3,4-Dihydro-2h-1,4-Benzoxazin-6-Yl)methyl]-3,4,5,6,7,8-Hexahydro[1]benzothieno[2,3-D]pyrimidine-2-Carboxamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor | PDB:3DNG | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
MLTPGNPKWE
89 RTNLTYRIRN99 YTPQLSEAEV109 ERAIKDAFEL119 WSVASPLIFT129 RISQGEADIN 139 IAFYQRDHGD149 NSPFDGPNGI159 LAHAFQPGQG169 IGGDAHFDAE179 ETWTNTSANY 189 NLFLVAAHEF199 GHSLGLAHSS209 DPGALMYPNY219 AFRETSNYSL229 PQDDIDGIQA 239 IYG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AXA or .AXA2 or .AXA3 or :3AXA;style chemicals stick;color identity;select .A:119 or .A:160 or .A:161 or .A:192 or .A:193 or .A:194 or .A:197 or .A:198 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:221 or .A:222 or .A:223 or .A:224 or .A:226 or .A:227 or .A:228 or .A:229 or .A:230; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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LEU119
4.756
LEU160
4.051
ALA161
4.708
PHE192
3.637
LEU193
3.238
VAL194
3.965
HIS197
3.506
GLU198
3.974
ALA213
3.397
LEU214
3.168
MET215
4.894
TYR216
2.915
PRO217
3.003
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Ligand Name: 2-Hydroxy-5-[4-(2-hydroxy-ethyl)-piperidin-1-YL]-5-phenyl-1H-pyrimidine-4,6-dione | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate Recognition | PDB:1JJ9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [10] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BBT or .BBT2 or .BBT3 or :3BBT;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:216 or .A:217 or .A:218 or .A:219; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: N-[(2r)-2-(Hydroxycarbamoyl)-4-Methylpentanoyl]-L-Alanylglycinamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | COMPLEX OF 1-HYDROXYLAMINE-2-ISOBUTYLMALONYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) | PDB:1JAQ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [11] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .01S or .01S2 or .01S3 or :301S;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: N-[(2s)-2-Benzyl-3-Sulfanylpropanoyl]-L-Alanylglycinamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | COMPLEX OF 3-MERCAPTO-2-BENZYLPROPANOYL-ALA-GLY-NH2 WITH THE CATALYTIC DOMAIN OF MATRIX METALLO PROTEINASE-8 (MET80 FORM) | PDB:1JAO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [11] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0D3 or .0D32 or .0D33 or :30D3;style chemicals stick;color identity;select .A:157 or .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:188 or .A:189 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASN157
4.484
GLY158
2.033
ILE159
3.594
LEU160
1.843
ALA161
3.091
HIS162
4.659
ALA163
4.948
ASN188
4.837
TYR189
3.135
LEU193
4.092
VAL194
3.716
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Ligand Name: N~2~-{3-[4-(5-Methylthiophen-2-Yl)phenyl]propanoyl}-L-Alpha-Glutamine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Human MMP8 in complex with L-glutamate motif inhibitor | PDB:3TT4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [12] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
GNPKWERTNL
93 TYRIRNYTPQ103 LSEAEVERAI113 KDAFELWSVA123 SPLIFTRISQ133 GEADINIAFY 143 QRDHGDNSPF153 DGPNGILAHA163 FQPGQGIGGD173 AHFDAEETWT183 NTSANYNLFL 193 VAAHEFGHSL203 GLAHSSDPGA213 LMYPNYAFRE223 TSNYSLPQDD233 IDGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E1S or .E1S2 or .E1S3 or :3E1S;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:213 or .A:214 or .A:215 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
3.725
ILE159
3.640
LEU160
2.750
ALA161
3.298
HIS162
4.266
LEU193
3.748
VAL194
4.092
HIS197
3.276
GLU198
2.782
HIS201
3.486
HIS207
2.952
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Ligand Name: N-Benzyl-N~2~-[(2r)-2-(Hydroxycarbamoyl)-4-Methylpentanoyl]-L-Alpha-Asparagine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | MMP8 WITH MALONIC AND ASPARTIC ACID BASED INHIBITOR | PDB:1A86 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [13] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0ZB or .0ZB2 or .0ZB3 or :30ZB;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: N~1~-(3-Aminobenzyl)-N~2~-[(2r)-2-(Hydroxycarbamoyl)-4-Methylpentanoyl]-L-Aspartamide | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | MMP8 WITH MALONIC AND ASPARAGINE BASED INHIBITOR | PDB:1A85 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [13] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0DY or .0DY2 or .0DY3 or :30DY;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:189 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLY158
2.021
ILE159
3.508
LEU160
1.792
ALA161
1.854
HIS162
3.342
ALA163
3.778
TYR189
3.790
LEU193
2.206
VAL194
2.817
HIS197
2.959
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Ligand Name: But-3-enyl-[5-(4-chloro-phenyl)-3,6-dihydro-[1,3,4]thiadiazin-2-ylidene]-amine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal Structure of MMP-8 complexed with a 6H-1,3,4-thiadiazine derived inhibitor | PDB:1JH1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | No | [14] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
NPKWERTNLT
94 YRIRNYTPQL104 SEAEVERAIK114 DAFELWSVAS124 PLIFTRISQG134 EADINIAFYQ 144 RDHGDNSPFD154 GPNGILAHAF164 QPGQGIGGDA174 HFDAEETWTN184 TSANYNLFLV 194 AAHEFGHSLG204 LAHSSDPGAL214 MYPNYAFRET224 SNYSLPQDDI234 DGIQAIYG |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .JST or .JST2 or .JST3 or :3JST;style chemicals stick;color identity;select .A:151 or .A:160 or .A:161 or .A:162 or .A:163 or .A:164 or .A:197 or .A:198 or .A:201 or .A:207 or .A:217; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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References | Top | ||||
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REF 1 | Extra binding region induced by non-zinc chelating inhibitors into the S1' subsite of matrix metalloproteinase 8 (MMP-8). J Med Chem. 2009 Feb 26;52(4):1040-9. | ||||
REF 2 | Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor. Biochemistry. 1995 Oct 31;34(43):14012-20. | ||||
REF 3 | 1.8-A crystal structure of the catalytic domain of human neutrophil collagenase (matrix metalloproteinase-8) complexed with a peptidomimetic hydroxamate primed-side inhibitor with a distinct selectivity profile. Eur J Biochem. 1997 Jul 1;247(1):356-63. | ||||
REF 4 | Structure of human neutrophil collagenase reveals large S1' specificity pocket. Nat Struct Biol. 1994 Feb;1(2):119-23. | ||||
REF 5 | Two crystal structures of human neutrophil collagenase, one complexed with a primed- and the other with an unprimed-side inhibitor: implications for drug design. J Med Chem. 2000 Sep 7;43(18):3377-85. | ||||
REF 6 | X-ray structure of the complex of the catalytic domain of MMP-8 and a bis-phosphonate inhibitor (ML115) | ||||
REF 7 | Catechol-based matrix metalloproteinase inhibitors with additional antioxidative activity. J Enzyme Inhib Med Chem. 2016;31(sup4):25-37. | ||||
REF 8 | Structural insight into the stereoselective inhibition of MMP-8 by enantiomeric sulfonamide phosphonates. J Med Chem. 2006 Feb 9;49(3):923-31. | ||||
REF 9 | N-Hydroxyurea as zinc binding group in matrix metalloproteinase inhibition: mode of binding in a complex with MMP-8. Bioorg Med Chem Lett. 2006 Jan 1;16(1):20-4. | ||||
REF 10 | The 1.8-A crystal structure of a matrix metalloproteinase 8-barbiturate inhibitor complex reveals a previously unobserved mechanism for collagenase substrate recognition. J Biol Chem. 2001 May 18;276(20):17405-12. | ||||
REF 11 | X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design. Eur J Biochem. 1995 Mar 15;228(3):830-41. | ||||
REF 12 | Simple pseudo-dipeptides with a P2' glutamate: a novel inhibitor family of matrix metalloproteases and other metzincins. J Biol Chem. 2012 Aug 3;287(32):26647-56. | ||||
REF 13 | Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data. Protein Sci. 1998 Jun;7(6):1303-9. | ||||
REF 14 | Structure-based design and synthesis of potent matrix metalloproteinase inhibitors derived from a 6H-1,3,4-thiadiazine scaffold. J Med Chem. 2001 Sep 27;44(20):3231-43. |
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