Structure of PDB 9at5 Chain B Binding Site BS01

Receptor Information

>9at5 Chain B (length=303) 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]

GSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM
LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTP
KYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVG
FNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTT
ITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDI
LGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ
CSG

Ligand information

Ligand ID

A1AGO

InChI

InChI=1S/C26H42F2N4O9S/c1-15(2)11-19(23(35)30-20(24(36)42(38,39)40)12-17-7-10-29-22(17)34)31-25(37)41-14-18-3-4-21(33)32(18)13-16-5-8-26(27,28)9-6-16/h15-20,24,36H,3-14H2,1-2H3,(H,29,34)(H,30,35)(H,31,37)(H,38,39,40)/t17-,18-,19-,20-,24+/m0/s1

InChIKey

RHYSFFXFVGVALZ-JZBNULMRSA-N

SMILES

Software	SMILES
CACTVS 3.385	CC(C)C[CH](NC(=O)OC[CH]1CCC(=O)N1CC2CCC(F)(F)CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
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)N2CC3CCC(CC3)(F)F
CACTVS 3.385	CC(C)C[C@H](NC(=O)OC[C@@H]1CCC(=O)N1CC2CCC(F)(F)CC2)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)N1CC1CCC(F)(F)CC1)C(O)S(=O)(=O)O
OpenEye OEToolkits 2.0.7	CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CCC(=O)N2CC3CCC(CC3)(F)F

Formula

C26 H42 F2 N4 O9 S

Name

(1R,2S)-2-({N-[({(2S)-1-[(4,4-difluorocyclohexyl)methyl]-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

9at5 Chain B 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	9at5 Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies.
Resolution	1.45 Å
Binding residue (original residue number in PDB)	H41 F140 N142 C145 H163 H164 M165 E166 P168 Q189
Binding residue (residue number reindexed from 1)	H42 F141 N143 C146 H164 H165 M166 E167 P169 Q190
Annotation score	1

External links

PDB	RCSB:9at5, PDBe:9at5, PDBj:9at5
PDBsum	9at5
PubMed	38953866
UniProt	P0DTD1\|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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