Structure of PDB 9at5 Chain A Binding Site BS02

Receptor Information

>9at5 Chain A (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]

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
GVT

Ligand information

Ligand ID

A1AGP

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-HPGFDKJQSA-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
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
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

Formula

C26 H42 F2 N4 O9 S

Name

(1S,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 A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

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)	F140 N142 G143 C145 H163 H164 M165 E166 P168 Q189 T190 A191
Binding residue (residue number reindexed from 1)	F139 N141 G142 C144 H162 H163 M164 E165 P167 Q188 T189 A190
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)

[Back to BioLiP]