Structure of PDB 5s28 Chain A Binding Site BS01

Receptor Information
>5s28 Chain A (length=165) 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]
SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL
Ligand information
Ligand IDWRV
InChIInChI=1S/C11H15FN2O2/c1-7-3-4-9(5-10(7)12)14-11(16)13-8(2)6-15/h3-5,8,15H,6H2,1-2H3,(H2,13,14,16)/t8-/m0/s1
InChIKeyONARABRJRRBWJE-QMMMGPOBSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H](CO)NC(=O)Nc1ccc(C)c(F)c1
OpenEye OEToolkits 2.0.7Cc1ccc(cc1F)NC(=O)NC(C)CO
CACTVS 3.385C[CH](CO)NC(=O)Nc1ccc(C)c(F)c1
ACDLabs 12.01N(C(C)CO)C(Nc1ccc(c(c1)F)C)=O
OpenEye OEToolkits 2.0.7Cc1ccc(cc1F)NC(=O)N[C@@H](C)CO
FormulaC11 H15 F N2 O2
NameN-(3-fluoro-4-methylphenyl)-N'-[(2S)-1-hydroxypropan-2-yl]urea
ChEMBL
DrugBank
ZINCZINC000040526072
PDB chain5s28 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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PDB5s28 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.09 Å
Binding residue
(original residue number in PDB)		D22 V24 E25 G48 V49 A52 F156
Binding residue
(residue number reindexed from 1)		D18 V20 E21 G44 V45 A48 F152
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:5s28, PDBe:5s28, PDBj:5s28
PDBsum5s28
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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