Structure of PDB 5spq Chain A Binding Site BS01

Receptor Information
>5spq 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 IDS63
InChIInChI=1S/C15H16ClN3O3/c1-15(14(21)22)3-5-19(8-15)11(20)6-9-7-18-13-12(9)10(16)2-4-17-13/h2,4,7H,3,5-6,8H2,1H3,(H,17,18)(H,21,22)/t15-/m1/s1
InChIKeyTVSPUBDQAPCPQX-OAHLLOKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1(CCN(C1)C(=O)Cc2c[nH]c3c2c(ccn3)Cl)C(=O)O
CACTVS 3.385C[C]1(CCN(C1)C(=O)Cc2c[nH]c3nccc(Cl)c23)C(O)=O
OpenEye OEToolkits 2.0.7C[C@]1(CCN(C1)C(=O)Cc2c[nH]c3c2c(ccn3)Cl)C(=O)O
ACDLabs 12.01CC1(CCN(C1)C(=O)Cc1c[NH]c2nccc(Cl)c21)C(=O)O
CACTVS 3.385C[C@]1(CCN(C1)C(=O)Cc2c[nH]c3nccc(Cl)c23)C(O)=O
FormulaC15 H16 Cl N3 O3
Name(3R)-1-[(4-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)acetyl]-3-methylpyrrolidine-3-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain5spq 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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PDB5spq Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Resolution1.05 Å
Binding residue
(original residue number in PDB)		G47 G48 V49 A129 G130 I131 F132 F156
Binding residue
(residue number reindexed from 1)		G45 G46 V47 A127 G128 I129 F130 F154
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:5spq, PDBe:5spq, PDBj:5spq
PDBsum5spq
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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