Structure of PDB 5xii Chain A Binding Site BS01

Receptor Information
>5xii Chain A (length=476) Species: 508771 (Toxoplasma gondii ME49) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVTAKKDENFSEWYTQAIVRSEMIEYYDISGCYIMRPWAFHIWEKVQRFF
DDEIKKMGVENSYFPMFVSRHKLEKGFSPEVAWVTHYGDSPLPEKIAIRP
TSETIMYPAYAKWIRSHRDLPLKLNQWCSVVRWEFKQPTPFLRTREFLWQ
EGHTAHATEEEAWELVLDILELYRRWYEECLAVPVIKGEKSEGEKFAGGK
KTTTVEAFIPENGRGIQAATSHLLGTNFAKMFEIEFEDEEGHKRLVHQTS
WGCTTRSLGVMIMTHGDDKGLVIPPRVASVQVVIIPILFTGEILGKCREL
KTMLEKADIRVRIDDRSNYTPGWKYNHWEVKGVPLRLELGPKDLAKGTAR
VVRRDTGEAYQISWADLAPKLLELMEGIQRSLFEKAKARLHEGIEKISTF
DEVMPALNRKHLVLAPWCEDPESEEQIKKETQKLSEITGAMKTLCIPFDQ
PPMPEGTKCFYTGKPAKRWTLWGRSY
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5xii Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		R470 E472 R481 T482 F485 Q555 T592 R594
Binding residue
(residue number reindexed from 1)		R132 E134 R143 T144 F147 Q217 T254 R256
Annotation score3
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5xii, PDBe:5xii, PDBj:5xii
PDBsum5xii
PubMed28867614
UniProtS8G8I1

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