Structure of PDB 7by6 Chain A Binding Site BS01

Receptor Information
>7by6 Chain A (length=299) Species: 5855 (Plasmodium vivax) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTYLLIKNEEYKKYQVKKYNFFSSGKKMNKGNIHLLIRQMRTFKDVFVSL
GFEEMNTHNYVESSFWCFDALYIPQQHPSRDLQDTFFIKVPEMCQEEFTD
QSYIENVKRVHSVGDYGSFGWNYQWELKSTKKNVLRTHTTANSCRALFQL
AKEYQKTGSIIPKKFFSIDRVFRNENLDSTHLAEFHQVEGLIIDRNLGLS
HLIGTLSAFYKYIGISKLRFKPTFNPYTEPSMEVYGYHEENKKWLEVGNS
GIFRPEMLRAMGFPPEVSVIAWGLSLERPTMIKYSIRNIRDLFGYRSVI
Ligand information
Ligand IDFB9
InChIInChI=1S/C34H37N3O5/c1-41-22-30-33(25-11-9-24(10-12-25)8-7-23-5-3-2-4-6-23)29-19-36(20-31(38)32(39)21-37(29)30)34(40)35-26-13-15-27(16-14-26)42-28-17-18-28/h2-6,9-16,28-33,38-39H,17-22H2,1H3,(H,35,40)/t29-,30+,31+,32-,33+/m0/s1
InChIKeyDJCBDEOPQMQGCA-AXJMTRDLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC[CH]1[CH]([CH]2CN(C[CH](O)[CH](O)CN12)C(=O)Nc3ccc(OC4CC4)cc3)c5ccc(cc5)C#Cc6ccccc6
OpenEye OEToolkits 2.0.7COCC1C(C2N1CC(C(CN(C2)C(=O)Nc3ccc(cc3)OC4CC4)O)O)c5ccc(cc5)C#Cc6ccccc6
OpenEye OEToolkits 2.0.7COC[C@@H]1[C@@H]([C@H]2N1C[C@@H]([C@@H](CN(C2)C(=O)Nc3ccc(cc3)OC4CC4)O)O)c5ccc(cc5)C#Cc6ccccc6
CACTVS 3.385COC[C@@H]1[C@@H]([C@@H]2CN(C[C@@H](O)[C@@H](O)CN12)C(=O)Nc3ccc(OC4CC4)cc3)c5ccc(cc5)C#Cc6ccccc6
FormulaC34 H37 N3 O5
Name(3S,4R,8R,9R,10S)-N-(4-cyclopropyloxyphenyl)-10-(methoxymethyl)-3,4-bis(oxidanyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7by6 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7by6 Structural basis of malaria parasite phenylalanine tRNA-synthetase inhibition by bicyclic azetidines.
Resolution2.997 Å
Binding residue
(original residue number in PDB)
I483 E516 V517 N519 S520 G543 L544 S545 R548 P549
Binding residue
(residue number reindexed from 1)
I213 E246 V247 N249 S250 G273 L274 S275 R278 P279
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.20: phenylalanine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004826 phenylalanine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006432 phenylalanyl-tRNA aminoacylation
GO:0043039 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:7by6, PDBe:7by6, PDBj:7by6
PDBsum7by6
PubMed33436639
UniProtA5K9S0|SYFA_PLAVS Phenylalanine--tRNA ligase alpha subunit (Gene Name=PVX_081300)

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