Structure of PDB 5rvf Chain A Binding Site BS01

Receptor Information
>5rvf 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 IDW8D
InChIInChI=1S/C10H13N5O/c11-9-8-10(13-5-12-8)15(6-14-9)4-7-2-1-3-16-7/h5-7H,1-4,11H2/t7-/m1/s1
InChIKeyGVRQWFFFCDLKPP-SSDOTTSWSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C3(CN2C=NC(=C1N=CN=C12)N)CCCO3
OpenEye OEToolkits 2.0.7c1nc-2c(ncn(c2n1)CC3CCCO3)N
CACTVS 3.385Nc1ncn(C[CH]2CCCO2)c3ncnc13
OpenEye OEToolkits 2.0.7c1nc-2c(ncn(c2n1)C[C@H]3CCCO3)N
CACTVS 3.385Nc1ncn(C[C@H]2CCCO2)c3ncnc13
FormulaC10 H13 N5 O
Name3-{[(2R)-oxolan-2-yl]methyl}-3H-purin-6-amine
ChEMBL
DrugBank
ZINC
PDB chain5rvf 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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PDB5rvf Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.0 Å
Binding residue
(original residue number in PDB)		D22 I23 V49 F156
Binding residue
(residue number reindexed from 1)		D20 I21 V47 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:5rvf, PDBe:5rvf, PDBj:5rvf
PDBsum5rvf
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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