Structure of PDB 7y3s Chain B Binding Site BS01

Receptor Information
>7y3s Chain B (length=483) 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
KQFAYQNSWGLTTRTIGVMTMVHGDNMGLVLPPRVACVQVVIIPCGISEE
DKEALIAKCNDYRRRLLSVNIRVRADLRDNYSPGWKFNHWELKGVPIRLE
VGPRDMKSCQFVAVRRDTGEKLTVAENEAETKLQAILEDIQVTLFTRASE
DLKTHMVVANTMEDFQKILDSGKIVQIPFCGEIDCEDWIKKTTAMGAKSL
CIPFKPLCELQPGAKCVCGKNPAKYYTLFGRSY
Ligand information
Ligand IDF9C
InChIInChI=1S/C15H19BrN4O2/c1-9-11(16)6-18-15-14(9)19-8-20(15)7-10(21)5-12-13(22)3-2-4-17-12/h6,8,12-13,17,22H,2-5,7H2,1H3/t12-,13+/m1/s1
InChIKeyHASBACODFIEZPY-OLZOCXBDSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c(Br)cnc2n(CC(=O)C[CH]3NCCC[CH]3O)cnc12
OpenEye OEToolkits 2.0.7Cc1c(cnc2c1ncn2CC(=O)C[C@@H]3[C@H](CCCN3)O)Br
OpenEye OEToolkits 2.0.7Cc1c(cnc2c1ncn2CC(=O)CC3C(CCCN3)O)Br
CACTVS 3.385Cc1c(Br)cnc2n(CC(=O)C[C@H]3NCCC[C@@H]3O)cnc12
FormulaC15 H19 Br N4 O2
Name1-(6-bromanyl-7-methyl-imidazo[4,5-b]pyridin-3-yl)-3-[(2R,3S)-3-oxidanylpiperidin-2-yl]propan-2-one
ChEMBL
DrugBank
ZINC
PDB chain7y3s Chain B 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]
PDB7y3s Control of fibrosis with enhanced safety via asymmetric inhibition of prolyl-tRNA synthetase 1.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		H1093 F1097 T1121 E1123 R1152 T1240 H1242 W1273 G1274
Binding residue
(residue number reindexed from 1)		H79 F83 T107 E109 R138 T226 H228 W259 G260
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:7y3s, PDBe:7y3s, PDBj:7y3s
PDBsum7y3s
PubMed37212275
UniProtP07814|SYEP_HUMAN Bifunctional glutamate/proline--tRNA ligase (Gene Name=EPRS1)

[Back to BioLiP]