Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T00442 | Target Info | |||
| Target Name | HUMAN catechol-O-methyl-transferase (COMT) | ||||
| Synonyms | S-COMT; MB-COMT; Catechol-O-methyltransferase; COMT | ||||
| Gene Name | COMT | ||||
| Biochemical Class | Methyltransferase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 3,5-Dinitrocatechol | Ligand Info | |||
| Canonical SMILES | C1=C(C=C(C(=C1[N+](=O)[O-])O)O)[N+](=O)[O-] | ||||
| InChI | 1S/C6H4N2O6/c9-5-2-3(7(11)12)1-4(6(5)10)8(13)14/h1-2,9-10H | ||||
| InChIKey | VDCDWNDTNSWDFJ-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 3870203 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6I3C Crystal structure of Human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and S-adensoyl-L-methionine | ||||||
| Method | X-ray diffraction | Resolution | 1.34 Å | Mutation | No | [1] |
| PDB Sequence |
GDTKEQRILN
11 HVLQHAEPGN21 AQSVLEAIDT31 YCEQKEWAMN41 VGDKKGKIVD51 AVIQEHQPSV 61 LLELGAYCGY71 SAVRMARLLS81 PGARLITIEI91 NPDCAAITQR101 MVDFAGVKDK 111 VTLVVGASQD121 IIPQLKKKYD131 VDTLDMVFLD141 HWKDRYLPDT151 LLLEECGLLR 161 KGTVLLADNV171 ICPGAPDFLA181 HVRGSSCFEC191 THYQSFLEYR201 EVVDGLEKAI 211 YKGP
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| PDB ID: 6I3D Crystal structure of Human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and Sinefungin | ||||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [1] |
| PDB Sequence |
GDTKEQRILN
11 HVLQHAEPGN21 AQSVLEAIDT31 YCEQKEWAMN41 VGDKKGKIVD51 AVIQEHQPSV 61 LLELGAYCGY71 SAVRMARLLS81 PGARLITIEI91 NPDCAAITQR101 MVDFAGVKDK 111 VTLVVGASQD121 IIPQLKKKYD131 VDTLDMVFLD141 HWKDRYLPDT151 LLLEECGLLR 161 KGTVLLADNV171 ICPGAPDFLA181 HVRGSSCFEC191 THYQSFLEYR201 EVVDGLEKAI 211 YKGP
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| PDB ID: 5LSA human catechol O-methyltransferase in complex with SAM and DNC at 1.50A | ||||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [2] |
| PDB Sequence |
DTKEQRILNH
62 VLQHAEPGNA72 QSVLEAIDTY82 CEQKEWAMNV92 GDKKGKIVDA102 VIQEHQPSVL 112 LELGAYCGYS122 AVRMARLLSP132 GARLITIEIN142 PDCAAITQRM152 VDFAGVKDKV 162 TLVVGASQDI172 IPQLKKKYDV182 DTLDMVFLDH192 WKDRYLPDTL202 LLEECGLLRK 212 GTVLLADNVI222 CPGAPDFLAH232 VRGSSCFECT242 HYQSFLEYRE252 VVDGLEKAIY 262 KGPG
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| PDB ID: 3A7E Crystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol | ||||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [3] |
| PDB Sequence |
DTKEQRILNH
12 VLQHAEPGNA22 QSVLEAIDTY32 CEQKEWAMNV42 GDKKGKIVDA52 VIQEHQPSVL 62 LELGAYCGYS72 AVRMARLLSP82 GARLITIEIN92 PDCAAITQRM102 VDFAGVKDKV 112 TLVVGASQDI122 IPQLKKKYDV132 DTLDMVFLDH142 WKDRYLPDTL152 LLEECGLLRK 162 GTVLLADNVI172 CPGAPDFLAH182 VRGSSCFECT192 HYQSFLEYRE202 VVDGLEKAIY 212 KG
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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 .DNC or .DNC2 or .DNC3 or :3DNC;style chemicals stick;color identity;select .A:38 or .A:40 or .A:41 or .A:46 or .A:141 or .A:142 or .A:143 or .A:144 or .A:169 or .A:170 or .A:173 or .A:174 or .A:198 or .A:199; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3BWY Crystal Structure of Human 108M Catechol O-methyltransferase bound with S-adenosylmethionine and inhibitor dinitrocatechol | ||||||
| Method | X-ray diffraction | Resolution | 1.30 Å | Mutation | No | [4] |
| PDB Sequence |
GDTKEQRILN
11 HVLQHAEPGN21 AQSVLEAIDT31 YCEQKEWAMN41 VGDKKGKIVD51 AVIQEHQPSV 61 LLELGAYCGY71 SAVRMARLLS81 PGARLITIEI91 NPDCAAITQR101 MVDFAGMKDK 111 VTLVVGASQD121 IIPQLKKKYD131 VDTLDMVFLD141 HWKDRYLPDT151 LLLEECGLLR 161 KGTVLLADNV171 ICPGAPDFLA181 HVRGSSCFEC191 THYQSFLEYR201 EVVDGLEKAI 211 YKGP
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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 .DNC or .DNC2 or .DNC3 or :3DNC;style chemicals stick;color identity;select .A:38 or .A:40 or .A:41 or .A:46 or .A:141 or .A:142 or .A:143 or .A:144 or .A:169 or .A:170 or .A:173 or .A:174 or .A:198 or .A:199; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 3BWM Crystal Structure of Human Catechol O-Methyltransferase with bound SAM and DNC | ||||||
| Method | X-ray diffraction | Resolution | 1.98 Å | Mutation | No | [4] |
| PDB Sequence |
GDTKEQRILN
11 HVLQHAEPGN21 AQSVLEAIDT31 YCEQKEWAMN41 VGDKKGKIVD51 AVIQEHQPSV 61 LLELGAYCGY71 SAVRMARLLS81 PGARLITIEI91 NPDCAAITQR101 MVDFAGVKDK 111 VTLVVGASQD121 IIPQLKKKYD131 VDTLDMVFLD141 HWKDRYLPDT151 LLLEECGLLR 161 KGTVLLADNV171 ICPGAPDFLA181 HVRGSSCFEC191 THYQSFLEYR201 EVVDGLEKAI 211 YKGP
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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 .DNC or .DNC2 or .DNC3 or :3DNC;style chemicals stick;color identity;select .A:38 or .A:40 or .A:41 or .A:46 or .A:141 or .A:142 or .A:143 or .A:144 or .A:169 or .A:170 or .A:173 or .A:174 or .A:198 or .A:199; 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 | Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol-O-methyltransferase. ACS Catal. 2019 May 3;9(5):4394-4401. | ||||
| REF 2 | human catechol O-methyltransferase in complex with SAM and DNC at 1.50A | ||||
| REF 3 | Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 1: In silico Fragments Linking and Verification of Spatial Proximity using Inter Ligand NOE Approachs | ||||
| REF 4 | Crystal structures of human 108V and 108M catechol O-methyltransferase. J Mol Biol. 2008 Jun 27;380(1):120-30. | ||||
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