Structure of PDB 5ekd Chain B Binding Site BS01

Receptor Information
>5ekd Chain B (length=327) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQKDSKKRVFSGIQPTGILHLGNYLGAIESWVRLQDEYDSVLYSIVDLHS
ITVPQDPAVLRQSILDMTAVLLACGINPEKSILFQQSQVSEHTQLSWILS
CMVRLPRLQHLHQWKAKTTGTVGLLTYPVLQAADILLYKSTHVPVGEDQV
QHMELVQDLAQGFNKKYGEFFPVPESILTSMKKVKSLRDPSAKMSKSDPD
KLATVRITDSPEEIVQKFRKAVTDFTSEVTYDPAGRAGVSNIVAVHAAVT
GLSVEEVVRRSAGMNTARYKLAVADAVIEKFAPIKREIEKLKLDKDHLEK
VLQIGSAKAKELAYTVCQEVKKLVGFL
Ligand information
Ligand ID5BX
InChIInChI=1S/C14H15N3O2/c1-8(12-13(18)17-14(15-2)19-12)10-7-16-11-6-4-3-5-9(10)11/h3-8,12,16H,1-2H3,(H,15,17,18)/t8-,12+/m1/s1
InChIKeyGNTVWGDQPXCYBV-PELKAZGASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C[C@H](c1c[nH]c2c1cccc2)[C@H]3C(=O)N=C(O3)NC
CACTVS 3.385CNC1=NC(=O)[C@@H](O1)[C@H](C)c2c[nH]c3ccccc23
ACDLabs 12.01CNC=1OC(C(N=1)=O)C(c2c3c(nc2)cccc3)C
CACTVS 3.385CNC1=NC(=O)[CH](O1)[CH](C)c2c[nH]c3ccccc23
OpenEye OEToolkits 1.9.2CC(c1c[nH]c2c1cccc2)C3C(=O)N=C(O3)NC
FormulaC14 H15 N3 O2
Name(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one;
Indolemycin;
Indolmycin
ChEMBLCHEMBL417852
DrugBank
ZINCZINC000003964188
PDB chain5ekd Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ekd Binding of Mg2+ATP Enhances Inhibition of Human Mitochondrial Tryptophanyl-tRNA Synthetase by Indolmycin
Resolution1.82 Å
Binding residue
(original residue number in PDB)		F38 G40 Q42 V74 H77 Y160 Q164 I168 V176 Q182
Binding residue
(residue number reindexed from 1)		F10 G12 Q14 V46 H49 Y127 Q131 I135 V143 Q149
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K145 K226 K229
Catalytic site (residue number reindexed from 1) K117 K193 K196
Enzyme Commision number 6.1.1.2: tryptophan--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004830 tryptophan-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0001570 vasculogenesis
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-tRNA aminoacylation
GO:0045766 positive regulation of angiogenesis
GO:0070183 mitochondrial tryptophanyl-tRNA aminoacylation
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ekd, PDBe:5ekd, PDBj:5ekd
PDBsum5ekd
PubMed
UniProtQ9UGM6|SYWM_HUMAN Tryptophan--tRNA ligase, mitochondrial (Gene Name=WARS2)

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