Structure of PDB 5rvd Chain A Binding Site BS01

Receptor Information
>5rvd 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 IDW7Y
InChIInChI=1S/C14H18N4/c1-3-10(4-1)12-5-2-8-18(12)14-11-6-7-15-13(11)16-9-17-14/h6-7,9-10,12H,1-5,8H2,(H,15,16,17)/t12-/m1/s1
InChIKeyBDDRHCCHCFMOJZ-GFCCVEGCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1c[nH]c2c1c(ncn2)N3CCC[C@@H]3C4CCC4
OpenEye OEToolkits 2.0.7c1c[nH]c2c1c(ncn2)N3CCCC3C4CCC4
CACTVS 3.385C1CC(C1)[C@H]2CCCN2c3ncnc4[nH]ccc34
CACTVS 3.385C1CC(C1)[CH]2CCCN2c3ncnc4[nH]ccc34
ACDLabs 12.01c1(ncnc2nccc12)N4C(C3CCC3)CCC4
FormulaC14 H18 N4
Name4-[(2R)-2-cyclobutylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine
ChEMBL
DrugBank
ZINC
PDB chain5rvd 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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PDB5rvd 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 G130 I131 F156 L160
Binding residue
(residue number reindexed from 1)		D20 I21 V47 G128 I129 F154 L158
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:5rvd, PDBe:5rvd, PDBj:5rvd
PDBsum5rvd
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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