Structure of PDB 5ujj Chain B Binding Site BS01

Receptor Information
>5ujj Chain B (length=388) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFVDPWTVQTSSAKGIDYDKLIVRFGSSKIDKELINRIERATGQRPHRFL
RRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTKW
LQDVFNVPLVIQMTDDEKYLWKDLTLDQAYSYAVENAKDIIACGFDINKT
FIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFPA
IQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPKP
ALLHSTFFPALQGAQTKMSASDPNSSIFLTDTAKQIKTKVNKHAFSGGRD
TIEEHRQFGGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELKK
ALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLSFDF
Ligand information
Ligand IDTYM
InChIInChI=1S/C21H24N7O8P/c22-12(5-10-6-24-13-4-2-1-3-11(10)13)21(31)36-37(32,33)34-7-14-16(29)17(30)20(35-14)28-9-27-15-18(23)25-8-26-19(15)28/h1-4,6,8-9,12,14,16-17,20,24,29-30H,5,7,22H2,(H,32,33)(H2,23,25,26)/t12-,14+,16+,17+,20+/m0/s1
InChIKeyIFQVDHDRFCKAAW-SQIXAUHQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](Cc1c[nH]c2ccccc12)C(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)CC(C(=O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N
ACDLabs 10.04O=C(OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc5c4ccccc4nc5
OpenEye OEToolkits 1.5.0c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N
CACTVS 3.341N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45
FormulaC21 H24 N7 O8 P
NameTRYPTOPHANYL-5'AMP
ChEMBL
DrugBankDB01831
ZINCZINC000016051386
PDB chain5ujj Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ujj An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y159 T160 G161 R162 G163 G172 H173 P176 Q194 E199 Q284 C309 A310 D312 Q313 F339 F340 K349 M350
Binding residue
(residue number reindexed from 1)		Y77 T78 G79 R80 G81 G90 H91 P94 Q112 E117 Q202 C227 A228 D230 Q231 F257 F258 K267 M268
Annotation score2
Enzymatic activity
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:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0019210 kinase inhibitor activity
GO:0019901 protein kinase binding
GO:0019904 protein domain specific binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0001525 angiogenesis
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006436 tryptophanyl-tRNA aminoacylation
GO:0006469 negative regulation of protein kinase activity
GO:0008285 negative regulation of cell population proliferation
GO:0010628 positive regulation of gene expression
GO:0031334 positive regulation of protein-containing complex assembly
GO:0045765 regulation of angiogenesis
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0070062 extracellular exosome

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ujj, PDBe:5ujj, PDBj:5ujj
PDBsum5ujj
PubMed28910573
UniProtP23381|SYWC_HUMAN Tryptophan--tRNA ligase, cytoplasmic (Gene Name=WARS1)

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