Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T61746 | Target Info | |||
| Target Name | Cathepsin B (CTSB) | ||||
| Synonyms | Ctsb; Cathepsins B; Cathepsin-B; Cathepsin B1; CPSB; APPS; APP secretase | ||||
| Target Type | Preclinical Target | ||||
| Gene Name | CTSB | ||||
| Biochemical Class | Peptidase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 2-Aminoethanimidic Acid | Ligand Info | |||||
| Structure Description | Cathepsin B complexed with dipeptidyl nitrile inhibitor | PDB:1GMY | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
KLPASFDARE
9 QWPQCPTIKE19 IRDQGSCGSC29 WAFGAVEAIS39 DRICIHTNAH49 VSVEVSAEDL 59 LTCCGSMCGD69 GCNGGYPAEA79 WNFWTRKGLV89 SGGLYESHVG99 CRPYSIPPCE 109 HHVNGSRPPC119 TGEGDTPKCS129 KICEPGYSPT139 YKQDKHYGYN149 SYSVSNSEKD 159 IMAEIYKNGP169 VEGAFSVYSD179 FLLYKSGVYQ189 HVTGEMMGGH199 AIRILGWGVE 209 NGTPYWLVAN219 SWNTDWGDNG229 FFKILRGQDH239 CGIESEVVAG249 IPRT |
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| Ligand Name: 3-Methylphenylalanine | Ligand Info | |||||
| Structure Description | Cathepsin B complexed with dipeptidyl nitrile inhibitor | PDB:1GMY | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
KLPASFDARE
9 QWPQCPTIKE19 IRDQGSCGSC29 WAFGAVEAIS39 DRICIHTNAH49 VSVEVSAEDL 59 LTCCGSMCGD69 GCNGGYPAEA79 WNFWTRKGLV89 SGGLYESHVG99 CRPYSIPPCE 109 HHVNGSRPPC119 TGEGDTPKCS129 KICEPGYSPT139 YKQDKHYGYN149 SYSVSNSEKD 159 IMAEIYKNGP169 VEGAFSVYSD179 FLLYKSGVYQ189 HVTGEMMGGH199 AIRILGWGVE 209 NGTPYWLVAN219 SWNTDWGDNG229 FFKILRGQDH239 CGIESEVVAG249 IPRT |
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| Ligand Name: Diphenylacetic acid | Ligand Info | |||||
| Structure Description | Cathepsin B complexed with dipeptidyl nitrile inhibitor | PDB:1GMY | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
KLPASFDARE
9 QWPQCPTIKE19 IRDQGSCGSC29 WAFGAVEAIS39 DRICIHTNAH49 VSVEVSAEDL 59 LTCCGSMCGD69 GCNGGYPAEA79 WNFWTRKGLV89 SGGLYESHVG99 CRPYSIPPCE 109 HHVNGSRPPC119 TGEGDTPKCS129 KICEPGYSPT139 YKQDKHYGYN149 SYSVSNSEKD 159 IMAEIYKNGP169 VEGAFSVYSD179 FLLYKSGVYQ189 HVTGEMMGGH199 AIRILGWGVE 209 NGTPYWLVAN219 SWNTDWGDNG229 FFKILRGQDH239 CGIESEVVAG249 IPRT |
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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 .DFA or .DFA2 or .DFA3 or :3DFA;style chemicals stick;color identity;select .A:68 or .A:69 or .A:72 or .A:73 or .A:74 or .A:75 or .A:198; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: PMID27998201-Compound-22 | Ligand Info | |||||
| Structure Description | Cathepsin B in complex with the nitroxoline | PDB:3AI8 | ||||
| Method | X-ray diffraction | Resolution | 2.11 Å | Mutation | No | [2] |
| PDB Sequence |
LKLPASFDAR
8 EQWPQCPTIK18 EIRDQGSCGS28 CWAFGAVEAI38 SDRICIHTNA48 HVSVEVSAED 58 LLTCCGSMCG68 DGCNGGYPAE78 AWNFWTRKGL88 VSGGLYESHV98 GCRPYSIPPC 108 EHHVNGSRPP118 CTGEGDTPKC128 SKICEPGYSP138 TYKQDKHYGY148 NSYSVSNSEK 158 DIMAEIYKNG168 PVEGAFSVYS178 DFLLYKSGVY188 QHVTGEMMGG198 HAIRILGWGV 208 ENGTPYWLVA218 NSWNTDWGDN228 GFFKILRGQD238 HCGIESEVVA248 GIPRTD |
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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 .HNQ or .HNQ2 or .HNQ3 or :3HNQ;style chemicals stick;color identity;select .B:23 or .B:24 or .B:25 or .B:26 or .B:27 or .B:28 or .B:29 or .B:109 or .B:110 or .B:111 or .B:119 or .B:120 or .B:121 or .B:122 or .B:199 or .B:221; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-Pyridinethiol | Ligand Info | |||||
| Structure Description | Crystal Structure of the tetragonal form of human liver cathepsin B | PDB:2IPP | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [3] |
| PDB Sequence |
> Chain A
LPASFDAREQ 10 WPQCPTIKEI20 RDQGSCGSCW30 AFGAVEAISD40 RICIHTN> Chain B VSVEVSAEDL 59 LTCCGSMCGD69 GCNGGYPAEA79 WNFWTRKGLV89 SGGLYESHVG99 CRPYSIPPCE 109 HHVNGSRPPC119 TGEGDTPKCS129 KICEPGYSPT139 YKQDKHYGYN149 SYSVSNSEKD 159 IMAEIYKNGP169 VEGAFSVYSD179 FLLYKSGVYQ189 HVTGEMMGGH199 AIRILGWGVE 209 NGTPYWLVAN219 SWNTDWGDNG229 FFKILRGQDH239 CGIESEVVAG249 IPRTD |
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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 .PYS or .PYS2 or .PYS3 or :3PYS;style chemicals stick;color identity;select .A:23 or .A:27 or .A:28 or .A:29 or .A:30 or .B:72 or .B:73 or .B:198 or .B:199 or .B:200; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1-N'-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-1-N-[(1R)-1-thiophen-3-ylethyl]cyclobutane-1,1-dicarboxamide | Ligand Info | |||||
| Structure Description | Structure of CathB with covalently linked Compound 28 | PDB:6AY2 | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [4] |
| PDB Sequence |
KLPASFDARE
9 QWPQCPTIKE19 IRDQGSCGSC29 WAFGAVEAIS39 DRICIHTNAH49 VSVEVSAEDL 59 LTCCGSMCGD69 GCNGGYPAEA79 WNFWTRKGLV89 SGGLYESHVG99 CRPYSIPPCE 109 HHVNGSRPPC119 TGEGDTPKCS129 KICEPGYSPT139 YKQDKHYGYN149 SYSVSNSEKD 159 IMAEIYKNGP169 VEGAFSVYSD179 FLLYKSGVYQ189 HVTGEMMGGH199 AIRILGWGVE 209 NGTPYWLVAN219 SWNTDWGDNG229 FFKILRGQDH239 CGIESEVVAG249 IPRTD |
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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 .C1G or .C1G2 or .C1G3 or :3C1G;style chemicals stick;color identity;select .A:23 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .A:67 or .A:68 or .A:69 or .A:71 or .A:72 or .A:73 or .A:74 or .A:75 or .A:76 or .A:121 or .A:122 or .A:173 or .A:198 or .A:199 or .A:200; 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-[(3r)-4-Ethoxy-3-Hydroxy-4-Oxobutanoyl]-L-Isoleucyl-L-Proline | Ligand Info | |||||
| Structure Description | Crystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors | PDB:1CSB | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [5] |
| PDB Sequence |
> Chain A
LPASFDAREQ 10 WPQCPTIKEI20 RDQGSCGSCW30 AFGAVEAISD40 RICIHTN> Chain B VSVEVSAEDL 59 LTCCGSMCGD69 GCNGGYPAEA79 WNFWTRKGLV89 SGGLYESHVG99 CRPYSIPPCE 109 HHVNGSRPPC119 TGEGDTPKCS129 KICEPGYSPT139 YKQDKHYGYN149 SYSVSNSEKD 159 IMAEIYKNGP169 VEGAFSVYSD179 FLLYKSGVYQ189 HVTGEMMGGH199 AIRILGWGVE 209 NGTPYWLVAN219 SWNTDWGDNG229 FFKILRGQDH239 CGIESEVVAG249 IPRTD |
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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 .EP0 or .EP02 or .EP03 or :3EP0;style chemicals stick;color identity;select .A:23 or .A:24 or .A:25 or .A:26 or .A:27 or .A:28 or .A:29 or .A:30 or .B:72 or .B:73 or .B:74 or .B:76 or .B:110 or .B:111 or .B:119 or .B:121 or .B:122 or .B:173 or .B:176 or .B:196 or .B:197 or .B:198 or .B:199 or .B:200 or .B:221; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLN23[A]
2.331
GLY24[A]
3.173
SER25[A]
4.146
CYS26[A]
3.249
GLY27[A]
2.976
SER28[A]
3.348
CYS29[A]
1.815
TRP30[A]
3.086
ASN72[B]
4.842
GLY73[B]
3.344
GLY74[B]
3.090
PRO76[B]
4.149
HIS110[B]
2.726
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Identification of dipeptidyl nitriles as potent and selective inhibitors of cathepsin B through structure-based drug design. J Med Chem. 2001 Dec 20;44(26):4524-34. | ||||
| REF 2 | Novel mechanism of cathepsin?B inhibition by antibiotic nitroxoline and related compounds. ChemMedChem. 2011 Aug 1;6(8):1351-6. | ||||
| REF 3 | Crystal Structure of the tetragonal form of human liver cathepsin B | ||||
| REF 4 | Discovery of Peptidomimetic Antibody-Drug Conjugate Linkers with Enhanced Protease Specificity. J Med Chem. 2018 Feb 8;61(3):989-1000. | ||||
| REF 5 | Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors. Biochemistry. 1995 Apr 11;34(14):4791-7. | ||||
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