Structure of PDB 4mw5 Chain B Binding Site BS01

Receptor Information
>4mw5 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 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 chain4mw5 Chain B Residue 909 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mw5 Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Resolution2.347 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 Y472 V473 W474 D476 L478 F522
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 Y235 V236 W237 D239 L241 F285
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:4mw5, PDBe:4mw5, PDBj:4mw5
PDBsum4mw5
PubMed24743796
UniProtQ38C91

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