Structure of PDB 5ssn Chain A Binding Site BS01

Receptor Information
>5ssn Chain A (length=167) 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]
VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL
Ligand information
Ligand IDRS9
InChIInChI=1S/C19H17N3O5/c23-8-16-20-13-5-4-9(6-14(13)21-16)18(25)22-17-10-2-1-3-15(24)11(10)7-12(17)19(26)27/h1-6,12,17,23-24H,7-8H2,(H,20,21)(H,22,25)(H,26,27)/t12-,17-/m0/s1
InChIKeyCXHYRAPCOSLYMC-SJCJKPOMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OCc1[nH]c2ccc(cc2n1)C(=O)N[C@@H]3[C@H](Cc4c(O)cccc34)C(O)=O
OpenEye OEToolkits 2.0.7c1cc2c(c(c1)O)CC(C2NC(=O)c3ccc4c(c3)nc([nH]4)CO)C(=O)O
CACTVS 3.385OCc1[nH]c2ccc(cc2n1)C(=O)N[CH]3[CH](Cc4c(O)cccc34)C(O)=O
ACDLabs 12.01O=C(O)C1Cc2c(cccc2O)C1NC(=O)c1cc2nc(CO)[NH]c2cc1
OpenEye OEToolkits 2.0.7c1cc2c(c(c1)O)C[C@@H]([C@H]2NC(=O)c3ccc4c(c3)nc([nH]4)CO)C(=O)O
FormulaC19 H17 N3 O5
Name(1R,2S)-4-hydroxy-1-{[2-(hydroxymethyl)-1H-benzimidazole-5-carbonyl]amino}-2,3-dihydro-1H-indene-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain5ssn Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ssn Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Resolution1.15 Å
Binding residue
(original residue number in PDB)		G48 V49 A52 L126 S128 A129 G130 F132
Binding residue
(residue number reindexed from 1)		G46 V47 A50 L124 S126 A127 G128 F130
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.-
External links
PDB RCSB:5ssn, PDBe:5ssn, PDBj:5ssn
PDBsum5ssn
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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