Structure of PDB 4py2 Chain A Binding Site BS01

Receptor Information
>4py2 Chain A (length=495) Species: 359391 (Brucella abortus 2308) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
REKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTDE
HGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERHY
KASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGPQ
GTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKSG
LKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERWA
YWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRIDPFE
LVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQRS
LSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLALG
AIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQPF
IPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY
Ligand information
Ligand ID43E
InChIInChI=1S/C15H17Cl2N3OS/c16-12-6-11(7-13(17)8-12)9-18-3-1-4-19-15(21)20-14-2-5-22-10-14/h2,5-8,10,18H,1,3-4,9H2,(H2,19,20,21)
InChIKeyDGBJLEREWKGWML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1cscc1NC(=O)NCCCNCc2cc(cc(c2)Cl)Cl
ACDLabs 12.01O=C(NCCCNCc1cc(Cl)cc(Cl)c1)Nc2ccsc2
CACTVS 3.370Clc1cc(Cl)cc(CNCCCNC(=O)Nc2cscc2)c1
FormulaC15 H17 Cl2 N3 O S
Name1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea
ChEMBLCHEMBL2159535
DrugBank
ZINCZINC000095580149
PDB chain4py2 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4py2 Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		A11 I12 Y14 D51 H53 G54 M227 Y228 V229 W230 D232 I265 F268 H269
Binding residue
(residue number reindexed from 1)		A9 I10 Y12 D49 H51 G52 M225 Y226 V227 W228 D230 I263 F266 H267
Annotation score1
Binding affinityMOAD: ic50=0.272uM
PDBbind-CN: -logKd/Ki=6.57,IC50=0.272uM
Enzymatic activity
Catalytic site (original residue number in PDB) I12 H20 H23 D51 S128 D131 G150 W230 I265
Catalytic site (residue number reindexed from 1) I10 H18 H21 D49 S126 D129 G148 W228 I263
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:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006431 methionyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4py2, PDBe:4py2, PDBj:4py2
PDBsum4py2
PubMed27500735
UniProtQ2YQ76

[Back to BioLiP]