Structure of PDB 5k0t Chain A Binding Site BS01

Receptor Information
>5k0t Chain A (length=496) Species: 204722 (Brucella suis 1330) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SREKYYITTAIAYPNGKPHIGHAYELIATDAMARFQRLNGMDVYFLTGTD
EHGIKMLQSARKEGITPRDLADRNTSAFRRMAEVLNSSNDDYIRTSEERH
YKASQAIWQAMVANGDIYKGGYAGWYSVRDEAYYGEEETEVRADGVRYGP
QGTPVEWVEEESYFFRLSAYQDKLLDLYENNPGFIMPAERRNEIVSFVKS
GLKDLSISRTTFDWGIPVPGDEKHVMYVWVDALTNYITALGYPDTTDERW
AYWPANAHIIGKDISRFHAVYWPAFLMSAQLPLPKRVFAHGFLFNRIDPF
ELVERYGLDQLRYFLMREVPFGQDGSYSHEAIVNRTNADLANDLGNLAQR
SLSMIAKNCEGKVPQPGAFSEADKAILDQADAALETARKAMDDQALHLAL
GAIFAVVAEANRYFAGQEPWALRKTDPARMGTVLYVTAEVLRRVGIMVQP
FIPQSAEKLLDILAVPADKRQFADVLASPLAGGTDLPAPQPVFPRY
Ligand information
Ligand ID415
InChIInChI=1S/C18H22ClN3O2/c1-24-17-11-14(10-15(19)12-17)13-20-8-5-9-21-18(23)22-16-6-3-2-4-7-16/h2-4,6-7,10-12,20H,5,8-9,13H2,1H3,(H2,21,22,23)
InChIKeyUCQXABGZXQUVHG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2COc1cc(cc(c1)Cl)CNCCCNC(=O)Nc2ccccc2
CACTVS 3.370COc1cc(Cl)cc(CNCCCNC(=O)Nc2ccccc2)c1
ACDLabs 12.01Clc1cc(cc(OC)c1)CNCCCNC(=O)Nc2ccccc2
FormulaC18 H22 Cl N3 O2
Name1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea
ChEMBLCHEMBL2159513
DrugBank
ZINCZINC000095573697
PDB chain5k0t Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5k0t Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		I12 Y14 D51 H53 G54 Y228 V229 W230 A233 I265 F268 H269
Binding residue
(residue number reindexed from 1)		I11 Y13 D50 H52 G53 Y227 V228 W229 A232 I264 F267 H268
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.78,IC50=1.657uM
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) I11 H19 H22 D50 S127 D130 G149 W229 I264
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5k0t, PDBe:5k0t, PDBj:5k0t
PDBsum5k0t
PubMed27500735
UniProtP59078|SYM_BRUSU Methionine--tRNA ligase (Gene Name=metG)

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