Structure of PDB 7y28 Chain A Binding Site BS01

Receptor Information
>7y28 Chain A (length=480) 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
QFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCALSEED
KEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLEV
GPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASED
LKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTARGAKSLC
IPFKPLCELQPGAKCVCNPAKYYTLFGRSY
Ligand information
Ligand IDF96
InChIInChI=1S/C21H22FN3O2/c22-16-4-1-3-14(9-16)15-6-7-18-20(10-15)25(13-24-18)12-17(26)11-19-21(27)5-2-8-23-19/h1,3-4,6-7,9-10,13,19,21,23,27H,2,5,8,11-12H2/t19-,21+/m1/s1
InChIKeyVQOVGCNWRLIDFU-CTNGQTDRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(cc(c1)F)c2ccc3c(c2)n(cn3)CC(=O)C[C@@H]4[C@H](CCCN4)O
CACTVS 3.385O[C@H]1CCCN[C@@H]1CC(=O)Cn2cnc3ccc(cc23)c4cccc(F)c4
OpenEye OEToolkits 2.0.7c1cc(cc(c1)F)c2ccc3c(c2)n(cn3)CC(=O)CC4C(CCCN4)O
CACTVS 3.385O[CH]1CCCN[CH]1CC(=O)Cn2cnc3ccc(cc23)c4cccc(F)c4
FormulaC21 H22 F N3 O2
Name1-[6-(3-fluorophenyl)benzimidazol-1-yl]-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one
ChEMBL
DrugBank
ZINC
PDB chain7y28 Chain A Residue 2601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7y28 Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		L1087 H1093 F1097 V1101 P1120 T1121 E1123 R1152 H1173 F1216 H1242 S1272 W1273 G1274
Binding residue
(residue number reindexed from 1)		L72 H78 F82 V86 P105 T106 E108 R137 H158 F201 H227 S257 W258 G259
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7y28, PDBe:7y28, PDBj:7y28
PDBsum7y28
PubMed37212275
UniProtP07814|SYEP_HUMAN Bifunctional glutamate/proline--tRNA ligase (Gene Name=EPRS1)

[Back to BioLiP]