Structure of PDB 4mw9 Chain B Binding Site BS01

Receptor Information
>4mw9 Chain B (length=533) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVF
ALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIR
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVD
NPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRR
EVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTG
SRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSA
GLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRE
SGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAY
TEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAP
WKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVH
RKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand ID2EJ
InChIInChI=1S/C17H19N3OS/c1-2-14-5-3-6-15(11-14)12-18-8-4-9-19-17(21)20-16-7-10-22-13-16/h1,3,5-7,10-11,13,18H,4,8-9,12H2,(H2,19,20,21)
InChIKeyNIXVRUOYNFTKQD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(NCCCNCc1cccc(c1)C#C)Nc2cscc2
ACDLabs 12.01O=C(NCCCNCc1cccc(C#C)c1)Nc2ccsc2
OpenEye OEToolkits 1.7.6C#Cc1cccc(c1)CNCCCNC(=O)Nc2ccsc2
FormulaC17 H19 N3 O S
Name1-{3-[(3-ethynylbenzyl)amino]propyl}-3-thiophen-3-ylurea
ChEMBL
DrugBank
ZINCZINC000098208150
PDB chain4mw9 Chain B Residue 806 [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]
PDB4mw9 Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 Y472 V473 D476
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 Y238 V239 D242
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 S156 S159 K320 K323
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:4mw9, PDBe:4mw9, PDBj:4mw9
PDBsum4mw9
PubMed24743796
UniProtQ38C91

[Back to BioLiP]