Structure of PDB 5rvg Chain A Binding Site BS01

Receptor Information
>5rvg 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 IDW8J
InChIInChI=1S/C12H17N5O/c13-11-10-12(15-7-14-10)17(8-16-11)4-1-2-9-3-5-18-6-9/h7-9H,1-6,13H2/t9-/m0/s1
InChIKeyGTHFXQJDSWIMIA-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1nc-2c(ncn(c2n1)CCCC3CCOC3)N
CACTVS 3.385Nc1ncn(CCC[C@H]2CCOC2)c3ncnc13
CACTVS 3.385Nc1ncn(CCC[CH]2CCOC2)c3ncnc13
OpenEye OEToolkits 2.0.7c1nc-2c(ncn(c2n1)CCC[C@H]3CCOC3)N
ACDLabs 12.01C(CN2C=NC(=C1N=CN=C12)N)CC3COCC3
FormulaC12 H17 N5 O
Name3-{3-[(3S)-oxolan-3-yl]propyl}-3H-purin-6-amine
ChEMBL
DrugBank
ZINC
PDB chain5rvg 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]
PDB5rvg 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 A129 G130 F156 L160
Binding residue
(residue number reindexed from 1)		D20 I21 V47 A127 G128 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:5rvg, PDBe:5rvg, PDBj:5rvg
PDBsum5rvg
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]