Structure of PDB 5xii Chain D Binding Site BS02

Receptor Information
>5xii Chain D (length=474) Species: 508771 (Toxoplasma gondii ME49) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMVTAKKDENFSEWYTQAIVRSEMIEYYDISGCYIMRPWAFHIWEKVQRF
FDDEIKKMGVENSYFPMFVSRHKLEKGFSPEVAWVTHYGDSPLPEKIAIR
PTSETIMYPAYAKWIRSHRDLPLKLNQWCSVVRWEFKQPTPFLRTREFLW
QEGHTAHATEEEAWELVLDILELYRRWYEECLAVPVIKGEKSEGEKFAGG
KKTTTVEAFIPENGRGIQAATSHLLGTNFAKMFEIEFEDEEGHKRLVHQT
SWGCTTRSLGVMIMTHGDDKGLVIPPRVASVQVVIIPTGEILGKCRELKT
MLEKADIRVRIDDRSNYTPGWKYNHWEVKGVPLRLELGPKDLAKGTARVV
RRDTGEAYQISWADLAPKLLELMEGIQRSLFEKAKARLHEGIEKISTFDE
VMPALNRKHLVLAPWCEDPESEEQIKKETQKLSEIQGAMKTLCIPFDQPP
MPEGTKCFYTGKPAKRWTLWGRSY
Ligand information
Ligand ID86X
InChIInChI=1S/C16H17ClFN3O2/c17-11-7-10-14(8-12(11)18)20-9-21(16(10)23)6-2-3-13-15(22)4-1-5-19-13/h7-9,13,19H,1-6H2/t13-/m1/s1
InChIKeyAAHVYVICLLIXKC-CYBMUJFWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1c2c(cc(c1Cl)F)N=CN(C2=O)CCCC3C(=O)CCCN3
OpenEye OEToolkits 2.0.6c1c2c(cc(c1Cl)F)N=CN(C2=O)CCC[C@@H]3C(=O)CCCN3
CACTVS 3.385Fc1cc2N=CN(CCC[CH]3NCCCC3=O)C(=O)c2cc1Cl
CACTVS 3.385Fc1cc2N=CN(CCC[C@H]3NCCCC3=O)C(=O)c2cc1Cl
FormulaC16 H17 Cl F N3 O2
Name6-chloranyl-7-fluoranyl-3-[3-[(2R)-3-oxidanylidenepiperidin-2-yl]propyl]quinazolin-4-one
ChEMBL
DrugBank
ZINC
PDB chain5xii Chain D Residue 1004 [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]
PDB5xii Targeting Prolyl-tRNA Synthetase to Accelerate Drug Discovery against Malaria, Leishmaniasis, Toxoplasmosis, Cryptosporidiosis, and Coccidiosis
Resolution2.17 Å
Binding residue
(original residue number in PDB)		F415 E418 V419 P438 T439 E441 R470 W487 F534 H560
Binding residue
(residue number reindexed from 1)		F78 E81 V82 P101 T102 E104 R133 W150 F197 H223
Annotation score1
Binding affinityMOAD: ic50=72nM
Enzymatic activity
Enzyme Commision number 6.1.1.15: proline--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:5xii, PDBe:5xii, PDBj:5xii
PDBsum5xii
PubMed28867614
UniProtS8G8I1

[Back to BioLiP]