Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T99397 | Target Info | |||
| Target Name | Voltage-dependent anion-selective channel 1 (VDAC1) | ||||
| Synonyms | Porin 31HM; Porin 31HL; Plasmalemmal porin; Outer mitochondrial membrane protein porin 1 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | VDAC1 | ||||
| Biochemical Class | Eukaryotic mitochondrial porin | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: NADH | Ligand Info | |||||
| Structure Description | NOE based model of hVDAC-1 bound to beta-NADH in detergent micelles | PDB:6TIR | ||||
| Method | Solution NMR | Resolution | N.A. | Mutation | No | [1] |
| PDB Sequence |
MAVPPTYADL
10 GKSARDVFTK20 GYGFGLIKLD30 LKTKSENGLE40 FTSSGSANTE50 TTKVTGSLET 60 KYRWTEYGLT70 FTEKWNTDNT80 LGTEITVEDQ90 LARGLKLTFD100 SSFSPNTGKK 110 NAKIKTGYKR120 EHINLGCDMD130 FDIAGPSIRG140 ALVLGYEGWL150 AGYQMNFETA 160 KSRVTQSNFA170 VGYKTDEFQL180 HTNVNDGTEF190 GGSIYQKVNK200 KLETAVNLAW 210 TAGNSNTRFG220 IAAKYQIDPD230 ACFSAKVNNS240 SLIGLGYTQT250 LKPGIKLTLS 260 ALLDGKNVNA270 GGHKLGLGLE280 FQALE
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ARG15
2.341
VAL17
4.472
PHE18
2.190
THR19
2.473
LYS20
2.254
TYR22
2.596
GLN154
4.681
ASN168
4.890
ASN183
3.428
ASN185
2.660
GLU189
4.856
ASN207
3.244
ARG218
1.945
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| Ligand Name: Spermidine | Ligand Info | |||||
| Structure Description | Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group | PDB:5XDO | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [2] |
| PDB Sequence |
MAVPPTYADL
10 GKSARDVFTK20 GYGFGLIKLD30 LKTKSENGLE40 FTSSGSANTE50 TTKVTGSLET 60 KYRWTEYGLT70 FTEKWNTDNT80 LGTEITVEDQ90 LARGLKLTFD100 SSFSPNTGKK 110 NAKIKTGYKR120 EHINLGCDMD130 FDIAGPSIRG140 ALVLGYEGWL150 AGYQMNFETA 160 KSRVTQSNFA170 VGYKTDEFQL180 HTNVNDGTEF190 GGSIYQKVNK200 KLETAVNLAW 210 TAGNSNTRFG220 IAAKYQIDPD230 ACFSAKVNNS240 SLIGLGYTQT250 LKPGIKLTLS 260 ALLDGKNVNA270 GGHKLGLGLE280 FQA
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| Ligand Name: Dimyristoylphosphatidylcholine, DL- | Ligand Info | |||||
| Structure Description | The dynamic nature of the VDAC1 channels in bilayers: human VDAC1 at 2.7 Angstrom resolution | PDB:6G6U | ||||
| Method | X-ray diffraction | Resolution | 2.74 Å | Mutation | No | [3] |
| PDB Sequence |
AVPPTYADLG
11 KSARDVFTKG21 YGFGLIKLDL31 KTKSENGLEF41 TSSGSANTET51 TKVTGSLETK 61 YRWTEYGLTF71 TEKWNTDNTL81 GTEITVEDQL91 ARGLKLTFDS101 SFSPNTGKKN 111 AKIKTGYKRE121 HINLGCDMDF131 DIAGPSIRGA141 LVLGYEGWLA151 GYQMNFETAK 161 SRVTQSNFAV171 GYKTDEFQLH181 TNVNDGTEFG191 GSIYQKVNKK201 LETAVNLAWT 211 AGNSNTRFGI221 AAKYQIDPDA231 CFSAKVNNSS241 LIGLGYTQTL251 KPGIKLTLSA 261 LLDGKNVNAG271 GHKLGLGLEF281 QA
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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 .MC3 or .MC32 or .MC33 or :3MC3;style chemicals stick;color identity;select .A:180 or .A:181 or .A:182 or .A:190 or .A:192 or .A:193 or .A:194 or .A:208 or .A:210 or .A:211 or .A:212 or .A:213; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: n-HEXANE | Ligand Info | |||||
| Structure Description | Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group | PDB:5XDO | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [2] |
| PDB Sequence |
MAVPPTYADL
10 GKSARDVFTK20 GYGFGLIKLD30 LKTKSENGLE40 FTSSGSANTE50 TTKVTGSLET 60 KYRWTEYGLT70 FTEKWNTDNT80 LGTEITVEDQ90 LARGLKLTFD100 SSFSPNTGKK 110 NAKIKTGYKR120 EHINLGCDMD130 FDIAGPSIRG140 ALVLGYEGWL150 AGYQMNFETA 160 KSRVTQSNFA170 VGYKTDEFQL180 HTNVNDGTEF190 GGSIYQKVNK200 KLETAVNLAW 210 TAGNSNTRFG220 IAAKYQIDPD230 ACFSAKVNNS240 SLIGLGYTQT250 LKPGIKLTLS 260 ALLDGKNVNA270 GGHKLGLGLE280 FQA
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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 .HEX or .HEX2 or .HEX3 or :3HEX;style chemicals stick;color identity;select .A:118 or .A:120 or .A:123 or .A:125; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Octane | Ligand Info | |||||
| Structure Description | Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group | PDB:5XDO | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [2] |
| PDB Sequence |
MAVPPTYADL
10 GKSARDVFTK20 GYGFGLIKLD30 LKTKSENGLE40 FTSSGSANTE50 TTKVTGSLET 60 KYRWTEYGLT70 FTEKWNTDNT80 LGTEITVEDQ90 LARGLKLTFD100 SSFSPNTGKK 110 NAKIKTGYKR120 EHINLGCDMD130 FDIAGPSIRG140 ALVLGYEGWL150 AGYQMNFETA 160 KSRVTQSNFA170 VGYKTDEFQL180 HTNVNDGTEF190 GGSIYQKVNK200 KLETAVNLAW 210 TAGNSNTRFG220 IAAKYQIDPD230 ACFSAKVNNS240 SLIGLGYTQT250 LKPGIKLTLS 260 ALLDGKNVNA270 GGHKLGLGLE280 FQA
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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 .OCT or .OCT2 or .OCT3 or :3OCT;style chemicals stick;color identity;select .A:167 or .A:169 or .A:184 or .A:186 or .A:187 or .A:208 or .A:210 or .A:214 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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Pentane | Ligand Info | |||||
| Structure Description | Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group | PDB:5XDO | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [2] |
| PDB Sequence |
MAVPPTYADL
10 GKSARDVFTK20 GYGFGLIKLD30 LKTKSENGLE40 FTSSGSANTE50 TTKVTGSLET 60 KYRWTEYGLT70 FTEKWNTDNT80 LGTEITVEDQ90 LARGLKLTFD100 SSFSPNTGKK 110 NAKIKTGYKR120 EHINLGCDMD130 FDIAGPSIRG140 ALVLGYEGWL150 AGYQMNFETA 160 KSRVTQSNFA170 VGYKTDEFQL180 HTNVNDGTEF190 GGSIYQKVNK200 KLETAVNLAW 210 TAGNSNTRFG220 IAAKYQIDPD230 ACFSAKVNNS240 SLIGLGYTQT250 LKPGIKLTLS 260 ALLDGKNVNA270 GGHKLGLGLE280 FQA
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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 .LNK or .LNK2 or .LNK3 or :3LNK;style chemicals stick;color identity;select .A:153 or .A:169 or .A:196 or .A:197 or .A:198; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The Structural Basis for Low Conductance in the Membrane Protein VDAC upon beta-NADH Binding and Voltage Gating. Structure. 2020 Feb 4;28(2):206-214.e4. | ||||
| REF 2 | Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1. Protein Sci. 2017 Sep;26(9):1749-1758. | ||||
| REF 3 | The dynamic nature of the VDAC1 channels in bilayers as revealed by two crystal structures of the human isoform in bicelles at 2.7 and 3.3 Angstrom resolution: implications for VDAC1 voltage-dependent mechanism and for its oligomerization | ||||
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