Structure of PDB 7f9d Chain A Binding Site BS01

Receptor Information
>7f9d Chain A (length=493) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEAKKEENLADWYSQVITKSEMIEYHDISGCYILRPWAYAIWEAIKDFF
DAEIKKLGVENCYFPMFVSQSALEKEKTHVADFAPEVAWVTRSGKTELAE
PIAIRPTSETVMYPAYAKWVQSHRDLPIKLNQWCNVVRWEFKHPQPFLRT
REFLWQEGHSAFATMEEAAEEVLQILDLYAQVYEELLAIPVVKGRKTEKE
KFAGGDYTTTIEAFISASGRAIQGGTSHHLGQNFSKMFEIVFEDPKIPGE
KQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGSEED
KEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEV
GPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASED
LKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARDQDLEP
GAPSMGAKSLCIPFKPLCELQPGAKCVCGKNPAKYYTLFGRSY
Ligand information
Ligand ID1UI
InChIInChI=1S/C28H26FN5O3/c1-17-7-23(34-6-5-28(16-30,27(34)36)21-3-4-21)12-25(33-17)26(35)32-13-18-8-19(10-22(29)9-18)20-11-24(37-2)15-31-14-20/h7-12,14-15,21H,3-6,13H2,1-2H3,(H,32,35)/t28-/m1/s1
InChIKeyRXELMDABJFGOHE-MUUNZHRXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cncc(c1)c2cc(F)cc(CNC(=O)c3cc(cc(C)n3)N4CC[C](C#N)(C5CC5)C4=O)c2
OpenEye OEToolkits 2.0.7Cc1cc(cc(n1)C(=O)NCc2cc(cc(c2)F)c3cc(cnc3)OC)N4CCC(C4=O)(C#N)C5CC5
OpenEye OEToolkits 2.0.7Cc1cc(cc(n1)C(=O)NCc2cc(cc(c2)F)c3cc(cnc3)OC)N4CC[C@@](C4=O)(C#N)C5CC5
CACTVS 3.385COc1cncc(c1)c2cc(F)cc(CNC(=O)c3cc(cc(C)n3)N4CC[C@@](C#N)(C5CC5)C4=O)c2
FormulaC28 H26 F N5 O3
Name4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(5-methoxypyridin-3-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7f9d Chain A Residue 1901 [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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PDB7f9d Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis.
Resolution2.497 Å
Binding residue
(original residue number in PDB)		E1154 K1156 H1157 P1158 L1162 R1163 T1164 R1165 F1167 W1169 Q1237 G1239 T1240 T1276 R1278
Binding residue
(residue number reindexed from 1)		E140 K142 H143 P144 L148 R149 T150 R151 F153 W155 Q223 G225 T226 T262 R264
Annotation score1
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:7f9d, PDBe:7f9d, PDBj:7f9d
PDBsum7f9d
PubMed36854028
UniProtP07814|SYEP_HUMAN Bifunctional glutamate/proline--tRNA ligase (Gene Name=EPRS1)

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