Structure of PDB 4mvw Chain B Binding Site BS01

Receptor Information
>4mvw Chain B (length=536) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVF
ALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIR
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVD
KDGNPCKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEF
RRREVIRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNY
LTGSRLRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFL
LSAGLPLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFL
LRESGFSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSP
AAYTEEDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTD
MAPWKLVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVP
EVHRKGIENFEFGAVPPGTRLGPAVEGEVLFSKRST
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 chain4mvw Chain B Residue 807 [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]
PDB4mvw Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Resolution2.901 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 Y472 V473 W474 D476 L478 H523
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 Y241 V242 W243 D245 L247 H292
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 S159 S162 K323 K326
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:4mvw, PDBe:4mvw, PDBj:4mvw
PDBsum4mvw
PubMed24743796
UniProtQ38C91

[Back to BioLiP]