Structure of PDB 5srp Chain A Binding Site BS02

Receptor Information

>5srp 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

TFA

InChI

InChI=1S/C2HF3O2/c3-2(4,5)1(6)7/h(H,6,7)

InChIKey

DTQVDTLACAAQTR-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 12.01	FC(F)(F)C(=O)O
CACTVS 3.370	OC(=O)C(F)(F)F
OpenEye OEToolkits 1.7.0	C(=O)(C(F)(F)F)O

Formula

C2 H F3 O2

Name

trifluoroacetic acid

PDB chain

5srp Chain A Residue 202 [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	5srp Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Resolution	1.05 Å
Binding residue (original residue number in PDB)	A129 G130 V155 D157 L160
Binding residue (residue number reindexed from 1)	A127 G128 V153 D155 L158
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:5srp, PDBe:5srp, PDBj:5srp
PDBsum	5srp
PubMed	36598939
UniProt	P0DTD1\|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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