Structure of PDB 5vad Chain A Binding Site BS01

Receptor Information
>5vad Chain A (length=481) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFFD
AEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAEP
IAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRTR
EFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKEK
FAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGEK
QFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGILSEE
DKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLE
VGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASE
DLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTAMGAKSL
CIPFKPLCELQPGAKCVCNPAKYYTLFGRSY
Ligand information
Ligand ID91Y
InChIInChI=1S/C21H24N4O2/c26-20(14-6-2-1-3-7-14)25-19-18(22-10-11-23-19)21(27)24-17-12-15-8-4-5-9-16(15)13-17/h4-5,8-11,14,17H,1-3,6-7,12-13H2,(H,24,27)(H,23,25,26)
InChIKeyOOCYBEPYZJOAIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(Nc1nccnc1C(=O)NC2Cc3ccccc3C2)C4CCCCC4
OpenEye OEToolkits 2.0.6c1ccc2c(c1)CC(C2)NC(=O)c3c(nccn3)NC(=O)C4CCCCC4
ACDLabs 12.01N(c3c(C(=O)NC2Cc1c(cccc1)C2)nccn3)C(C4CCCCC4)=O
FormulaC21 H24 N4 O2
Name3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain5vad Chain A Residue 1601 [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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PDB5vad Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		R1152 E1154 F1161 L1162 R1163 T1164 F1167 W1169 T1240 T1276 R1278
Binding residue
(residue number reindexed from 1)		R137 E139 F146 L147 R148 T149 F152 W154 T225 T261 R263
Annotation score1
Binding affinityMOAD: Kd=0.76nM
PDBbind-CN: -logKd/Ki=9.12,Kd=0.76nM
Enzymatic activity
Enzyme Commision number 6.1.1.15: proline--tRNA ligase.
6.1.1.17: glutamate--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004827 proline-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006433 prolyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vad, PDBe:5vad, PDBj:5vad
PDBsum5vad
PubMed28501621
UniProtP07814|SYEP_HUMAN Bifunctional glutamate/proline--tRNA ligase (Gene Name=EPRS1)

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