Structure of PDB 4mvy Chain B Binding Site BS01

Receptor Information
>4mvy Chain B (length=530) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVF
ALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIR
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGVD
KVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVI
RAVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRL
RVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLP
LPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGF
SDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEE
DESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKL
VKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKG
IENFEFGAVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand ID387
InChIInChI=1S/C17H19Cl2N3O2/c18-13-7-12(8-14(19)9-13)11-20-5-2-6-21-17(24)22-15-3-1-4-16(23)10-15/h1,3-4,7-10,20,23H,2,5-6,11H2,(H2,21,22,24)
InChIKeyGNDFIQUTHVHDAI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Oc1cccc(NC(=O)NCCCNCc2cc(Cl)cc(Cl)c2)c1
ACDLabs 12.01Clc1cc(cc(Cl)c1)CNCCCNC(=O)Nc2cccc(O)c2
OpenEye OEToolkits 1.7.2c1cc(cc(c1)O)NC(=O)NCCCNCc2cc(cc(c2)Cl)Cl
FormulaC17 H19 Cl2 N3 O2
Name1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea
ChEMBLCHEMBL2159526
DrugBank
ZINCZINC000095580621
PDB chain4mvy 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]
PDB4mvy Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Resolution2.314 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 L456 Y472 V473 W474 D476 H523
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 L219 Y235 V236 W237 D239 H286
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 S153 S156 K317 K320
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:4mvy, PDBe:4mvy, PDBj:4mvy
PDBsum4mvy
PubMed24743796
UniProtQ38C91

[Back to BioLiP]