Structure of PDB 9at3 Chain A Binding Site BS01

Receptor Information

>9at3 Chain A (length=298) 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]

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

Ligand ID

A1AGK

InChI

InChI=1S/C27H46N4O9S/c1-17(2)14-21(25(34)29-22(26(35)41(37,38)39)15-19-10-12-28-24(19)33)30-27(36)40-16-20-8-9-23(32)31(20)13-11-18-6-4-3-5-7-18/h17-22,26,35H,3-16H2,1-2H3,(H,28,33)(H,29,34)(H,30,36)(H,37,38,39)/t19-,20-,21-,22-,26+/m0/s1

InChIKey

UKTOBRQSOYSYJK-LEUUJVKFSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CCC(=O)N2CCC3CCCCC3
OpenEye OEToolkits 2.0.7	CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC[C@@H]2CCC(=O)N2CCC3CCCCC3
CACTVS 3.385	CC(C)C[CH](NC(=O)OC[CH]1CCC(=O)N1CCC2CCCCC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
CACTVS 3.385	CC(C)C[C@H](NC(=O)OC[C@@H]1CCC(=O)N1CCC2CCCCC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O
ACDLabs 12.01	O=C1NCCC1CC(NC(=O)C(CC(C)C)NC(=O)OCC1CCC(=O)N1CCC1CCCCC1)C(O)S(=O)(=O)O

Formula

C27 H46 N4 O9 S

Name

(1R,2S)-2-{[N-({[(2S)-1-(2-cyclohexylethyl)-5-oxopyrrolidin-2-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

ChEMBL

DrugBank

ZINC

PDB chain

9at3 Chain A Residue 401 [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	9at3 Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.
Resolution	1.7 Å
Binding residue (original residue number in PDB)	H41 F140 N142 C145 H163 H164 M165 E166 P168 Q189 T190
Binding residue (residue number reindexed from 1)	H39 F138 N140 C143 H161 H162 M163 E164 P166 Q187 T188
Annotation score	1

External links

PDB	RCSB:9at3, PDBe:9at3, PDBj:9at3
PDBsum	9at3
PubMed	38953866
UniProt	P0DTD1\|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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