Structure of PDB 4mw1 Chain B Binding Site BS01

Receptor Information
>4mw1 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 ID44F
InChIInChI=1S/C16H20ClN3O2S/c1-22-15-8-12(7-13(17)9-15)10-18-4-2-5-19-16(21)20-14-3-6-23-11-14/h3,6-9,11,18H,2,4-5,10H2,1H3,(H2,19,20,21)
InChIKeyFARFGOOSWAQYQX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1cc(Cl)cc(CNCCCNC(=O)Nc2cscc2)c1
OpenEye OEToolkits 1.7.2COc1cc(cc(c1)Cl)CNCCCNC(=O)Nc2ccsc2
ACDLabs 12.01O=C(NCCCNCc1cc(OC)cc(Cl)c1)Nc2ccsc2
FormulaC16 H20 Cl N3 O2 S
Name1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-thiophen-3-ylurea
ChEMBLCHEMBL2159536
DrugBank
ZINCZINC000095580635
PDB chain4mw1 Chain B Residue 808 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mw1 Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Resolution2.494 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 Y472 V473 W474 D476 L478 I519
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 Y241 V242 W243 D245 L247 I288
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:4mw1, PDBe:4mw1, PDBj:4mw1
PDBsum4mw1
PubMed24743796
UniProtQ38C91

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