Structure of PDB 5rv2 Chain A Binding Site BS01

Receptor Information
>5rv2 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 IDW7S
InChIInChI=1S/C12H11N3O/c16-12(11-9-13-6-7-14-11)15-8-10-4-2-1-3-5-10/h1-7,9H,8H2,(H,15,16)
InChIKeyLCEYIUAAVRLLIN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(NCc1ccccc1)c2cnccn2
OpenEye OEToolkits 2.0.7c1ccc(cc1)CNC(=O)c2cnccn2
ACDLabs 12.01c2c(CNC(c1cnccn1)=O)cccc2
FormulaC12 H11 N3 O
NameN-benzylpyrazine-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000000311783
PDB chain5rv2 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5rv2 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.01 Å
Binding residue
(original residue number in PDB)		D22 G48 V49 A52 G130 F156
Binding residue
(residue number reindexed from 1)		D20 G46 V47 A50 G128 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:5rv2, PDBe:5rv2, PDBj:5rv2
PDBsum5rv2
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]