Structure of PDB 7gmd Chain A Binding Site BS01

Receptor Information
>7gmd Chain A (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF
Ligand information
Ligand IDR2X
InChIInChI=1S/C27H27ClN4O4/c28-19-8-5-7-17(14-19)24(26(34)30-21-16-29-15-18-6-1-2-9-20(18)21)31-25(33)22-10-11-23(36-22)27(35)32-12-3-4-13-32/h1-2,5-9,14-16,22-24H,3-4,10-13H2,(H,30,34)(H,31,33)/t22-,23+,24+/m0/s1
InChIKeyRZBYEPRBZPLACH-RBZQAINGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cncc2NC(=O)[C@@H](c3cccc(c3)Cl)NC(=O)[C@@H]4CC[C@@H](O4)C(=O)N5CCCC5
CACTVS 3.385Clc1cccc(c1)[CH](NC(=O)[CH]2CC[CH](O2)C(=O)N3CCCC3)C(=O)Nc4cncc5ccccc45
ACDLabs 12.01O=C(NC(c1cccc(Cl)c1)C(=O)Nc1cncc2ccccc21)C1CCC(O1)C(=O)N1CCCC1
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cncc2NC(=O)C(c3cccc(c3)Cl)NC(=O)C4CCC(O4)C(=O)N5CCCC5
CACTVS 3.385Clc1cccc(c1)[C@@H](NC(=O)[C@@H]2CC[C@@H](O2)C(=O)N3CCCC3)C(=O)Nc4cncc5ccccc45
FormulaC27 H27 Cl N4 O4
Name(2S,5R)-N-{(1R)-1-(3-chlorophenyl)-2-[(isoquinolin-4-yl)amino]-2-oxoethyl}-5-(pyrrolidine-1-carbonyl)oxolane-2-carboxamide (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain7gmd Chain A Residue 408 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7gmd Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.937 Å
Binding residue
(original residue number in PDB)
T25 H41 C44 S46 M49 F140 L141 C145 H163 M165 E166 D187 Q189
Binding residue
(residue number reindexed from 1)
T25 H41 C44 S46 M49 F140 L141 C145 H163 M165 E166 D187 Q189
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
2.1.1.57: methyltransferase cap1.
2.7.7.48: RNA-directed RNA polymerase.
2.7.7.50: mRNA guanylyltransferase.
3.1.13.-
3.4.19.12: ubiquitinyl hydrolase 1.
3.4.22.-
3.4.22.69: SARS coronavirus main proteinase.
3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
4.6.1.-
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

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Molecular Function

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Biological Process
External links
PDB RCSB:7gmd, PDBe:7gmd, PDBj:7gmd
PDBsum7gmd
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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