Structure of PDB 1r6u Chain A Binding Site BS01

Receptor Information
>1r6u Chain A (length=388) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDFVDPWTVQTSSAKGIDYDKLIVRFGSSKIDKELINRIERATGQRPHHF
LRRGIFFSHRDMNQVLDAYENKKPFYLYTGRGPSSEAMHVGHLIPFIFTK
WLQDVFNVPLVIQMTDDEKYLWKDLTLDQAYGDAVENAKDIIACGFDINK
TFIFSDLDYMGMSSGFYKNVVKIQKHVTFNQVKGIFGFTDSDCIGKISFP
AIQAAPSFSNSFPQIFRDRTDIQCLIPCAIDQDPYFRMTRDVAPRIGYPK
PALLHSTFFPALQGAQTKMSASDPNSSIFLTDTAKQIKTKVNKHAFSGGR
DTIEEHRQFGGNCDVDVSFMYLTFFLEDDDKLEQIRKDYTSGAMLTGELK
KALIEVLQPLIAEHQARRKEVTDEIVKEFMTPRKLSFD
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 chain1r6u Chain A 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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PDB1r6u Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y159 T160 G161 R162 G163 G172 P176 Q194 E199 Q284 A310 Q313 F340 M350
Binding residue
(residue number reindexed from 1)		Y78 T79 G80 R81 G82 G91 P95 Q113 E118 Q203 A229 Q232 F259 M269
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1r6u, PDBe:1r6u, PDBj:1r6u
PDBsum1r6u
PubMed17637340
UniProtP23381|SYWC_HUMAN Tryptophan--tRNA ligase, cytoplasmic (Gene Name=WARS1)

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