Structure of PDB 5dk4 Chain A Binding Site BS02

Receptor Information
>5dk4 Chain A (length=328) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQ
DPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYI
GELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQ
HIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPN
PKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLS
GQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRV
LDEGAEKANRVASEMVRKMEQAMGLGRR
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 chain5dk4 Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dk4 Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F5 S6 G7 Q9 H43 Y125 M129 D132 I133 V141 V143 Q147
Binding residue
(residue number reindexed from 1)		F6 S7 G8 Q10 H44 Y126 M130 D133 I134 V142 V144 Q148
Annotation score1
Binding affinityMOAD: Ki=2nM
PDBbind-CN: -logKd/Ki=8.70,Ki=2.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) K111 K192 K195
Catalytic site (residue number reindexed from 1) K112 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:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Biological Process
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Cellular Component
External links
PDB RCSB:5dk4, PDBe:5dk4, PDBj:5dk4
PDBsum5dk4
PubMed26555258
UniProtP00953|SYW_GEOSE Tryptophan--tRNA ligase (Gene Name=trpS)

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