Structure of PDB 7wpn Chain A Binding Site BS02

Receptor Information
>7wpn Chain A (length=478) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTDE
HGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERHK
HVVEQVFERLLKQGDIYLGEYLVKEESYFFNISKYTDRLLEFYDQNPDFI
QPPSRKNEMINNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALV
NYISALGYLSDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPL
PKKVFAHGWILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFG
SDGVFTPEAFVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHE
LDEEMEAMALETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWV
LAKDDSQKDMLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQ
FMEFSSLEQYGVLNESIMVTGQPKPIFP
Ligand information
Ligand ID29I
InChIInChI=1S/C33H31BrN4O6/c1-35-32(40)23-10-13-26-25(15-23)37-31(22-9-12-24(34)28(39)16-22)38(26)27(21-11-14-29(42-2)30(17-21)43-3)18-36-33(41)44-19-20-7-5-4-6-8-20/h4-17,27,39H,18-19H2,1-3H3,(H,35,40)(H,36,41)/t27-/m0/s1
InChIKeyJSBGVKZBZYECPF-MHZLTWQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)c1ccc2n([CH](CNC(=O)OCc3ccccc3)c4ccc(OC)c(OC)c4)c(nc2c1)c5ccc(Br)c(O)c5
OpenEye OEToolkits 2.0.7CNC(=O)c1ccc2c(c1)nc(n2C(CNC(=O)OCc3ccccc3)c4ccc(c(c4)OC)OC)c5ccc(c(c5)O)Br
OpenEye OEToolkits 2.0.7CNC(=O)c1ccc2c(c1)nc(n2[C@@H](CNC(=O)OCc3ccccc3)c4ccc(c(c4)OC)OC)c5ccc(c(c5)O)Br
CACTVS 3.385CNC(=O)c1ccc2n([C@@H](CNC(=O)OCc3ccccc3)c4ccc(OC)c(OC)c4)c(nc2c1)c5ccc(Br)c(O)c5
FormulaC33 H31 Br N4 O6
Name(phenylmethyl) N-[(2R)-2-[2-(4-bromanyl-3-oxidanyl-phenyl)-5-(methylcarbamoyl)benzimidazol-1-yl]-2-(3,4-dimethoxyphenyl)ethyl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain7wpn Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7wpn Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I12 Y14 D51 H53 G54 Y235 V236 A240 L241 F276
Binding residue
(residue number reindexed from 1)		I10 Y12 D49 H51 G52 Y193 V194 A198 L199 F234
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:7wpn, PDBe:7wpn, PDBj:7wpn
PDBsum7wpn
PubMed35474479
UniProtQ5HII6|SYM_STAAC Methionine--tRNA ligase (Gene Name=metG)

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