Structure of PDB 4mw6 Chain B Binding Site BS01

Receptor Information
>4mw6 Chain B (length=527) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVF
ALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIR
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDKVS
LESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAV
EKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLRVD
ESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPK
KIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDD
GDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDES
LIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKT
DPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIEN
FEFGAVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand ID2EE
InChIInChI=1S/C25H28ClN3O2S/c1-2-7-20-14-22(26)15-21(24(20)31-17-19-8-4-3-5-9-19)16-27-11-6-12-28-25(30)29-23-10-13-32-18-23/h2-5,8-10,13-15,18,27H,1,6-7,11-12,16-17H2,(H2,28,29,30)
InChIKeyPTVMLFAESGWFGV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCCCNCc2cc(Cl)cc(c2OCc1ccccc1)C/C=C)Nc3ccsc3
OpenEye OEToolkits 1.7.6C=CCc1cc(cc(c1OCc2ccccc2)CNCCCNC(=O)Nc3ccsc3)Cl
CACTVS 3.385Clc1cc(CNCCCNC(=O)Nc2cscc2)c(OCc3ccccc3)c(CC=C)c1
FormulaC25 H28 Cl N3 O2 S
Name1-(3-{[2-(benzyloxy)-5-chloro-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea
ChEMBL
DrugBank
ZINCZINC000098208148
PDB chain4mw6 Chain B Residue 806 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mw6 Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Resolution2.558 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 Y472 V473 W474 L478 F522
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 Y232 V233 W234 L238 F282
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H256 H259 S364 D367 S390 S393 K554 K557
Catalytic site (residue number reindexed from 1) H25 H28 S133 D136 S150 S153 K314 K317
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:4mw6, PDBe:4mw6, PDBj:4mw6
PDBsum4mw6
PubMed24743796
UniProtQ38C91

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