Structure of PDB 7wpi Chain A Binding Site BS01

Receptor Information
>7wpi Chain A (length=520) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGT
DEHGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEER
HKHVVEQVFERLLKQGDIYLGEYEGWYSVPDETYYTESQLVDPQYENGKI
IGGKSPDSGHEVELVKEESYFFNISKYTDRLLEFYDQNPDFIQPPSRKNE
MINNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALVNYISALGY
LSDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPLPKKVFAHG
WILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFGSDGVFTPE
AFVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHELDEEMEAM
ALETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWVLAKDDSQK
DMLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQFMEFSSLE
QYGVLNESIMVTGQPKPIFP
Ligand information
Ligand ID1V7
InChIInChI=1S/C37H39BrN4O6/c1-37(2,3)25-9-7-8-10-31(25)48-21-34(44)40-20-29(22-13-16-32(46-5)33(19-22)47-6)42-28-15-12-24(36(45)39-4)17-27(28)41-35(42)23-11-14-26(38)30(43)18-23/h7-19,29,43H,20-21H2,1-6H3,(H,39,45)(H,40,44)/t29-/m0/s1
InChIKeyNVXVCMOQLYUYSD-LJAQVGFWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccccc1OCC(=O)NCC(c2ccc(c(c2)OC)OC)n3c4ccc(cc4nc3c5ccc(c(c5)O)Br)C(=O)NC
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccccc1OCC(=O)NC[C@@H](c2ccc(c(c2)OC)OC)n3c4ccc(cc4nc3c5ccc(c(c5)O)Br)C(=O)NC
CACTVS 3.385CNC(=O)c1ccc2n([CH](CNC(=O)COc3ccccc3C(C)(C)C)c4ccc(OC)c(OC)c4)c(nc2c1)c5ccc(Br)c(O)c5
CACTVS 3.385CNC(=O)c1ccc2n([C@@H](CNC(=O)COc3ccccc3C(C)(C)C)c4ccc(OC)c(OC)c4)c(nc2c1)c5ccc(Br)c(O)c5
FormulaC37 H39 Br N4 O6
Name2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7wpi Chain A Residue 601 [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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PDB7wpi Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		I12 Y14 D51 H53 G54 E132 Y235 V236 W237 A240 L241 Y244 I273 F276 H277
Binding residue
(residue number reindexed from 1)		I12 Y14 D51 H53 G54 E132 Y235 V236 W237 A240 L241 Y244 I273 F276 H277
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.10: methionine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004825 methionine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006431 methionyl-tRNA aminoacylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7wpi, PDBe:7wpi, PDBj:7wpi
PDBsum7wpi
PubMed35474479
UniProtQ5HII6|SYM_STAAC Methionine--tRNA ligase (Gene Name=metG)

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