Structure of PDB 5rte Chain A Binding Site BS01

Receptor Information

>5rte 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 ID

4FL

InChI

InChI=1S/C8H7N3/c1-3-9-4-2-7(1)8-10-5-6-11-8/h1-6H,(H,10,11)

InChIKey

QWZSAEUNIBEKIZ-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.385	[nH]1ccnc1c2ccncc2
OpenEye OEToolkits 1.9.2	c1cnccc1c2[nH]ccn2
ACDLabs 12.01	c1c(ccnc1)c2nccn2

Formula

C8 H7 N3

Name

4-(1H-imidazol-2-yl)pyridine

PDB chain

5rte Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5rte Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution	1.0 Å
Binding residue (original residue number in PDB)	D22 G48 V49 A52 F156
Binding residue (residue number reindexed from 1)	D20 G46 V47 A50 F154
Annotation score	1

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:5rte, PDBe:5rte, PDBj:5rte
PDBsum	5rte
PubMed	33853786
UniProt	P0DTD1\|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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