Structure of PDB 6cml Chain B Binding Site BS01

Receptor Information
>6cml Chain B (length=529) Species: 185431 (Trypanosoma brucei brucei TREU927) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPGSMKVEKVFFVTSPIYYVNAAPHIGHVYSTLITDVIGRYHRVKGERVF
ALTGTDEHGQKVAEAAKQKQVSPYDFTTAVAGEFKKCFEQMDYSIDYFIR
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGCK
VSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIR
AVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLR
VDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPL
PKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFS
DDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEED
ESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLV
KTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGI
ENFEFGAVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand ID96S
InChIInChI=1S/C20H19Cl2N5O2/c1-3-27-13(8-12-4-5-14(29-2)9-15(12)21)10-26(20(27)28)11-18-23-16-6-7-17(22)24-19(16)25-18/h4-7,9-10H,3,8,11H2,1-2H3,(H,23,24,25)
InChIKeyRDYREYRDYHMQKI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc4c(CC=3N(C(=O)N(Cc2nc1c(nc(cc1)Cl)n2)C=3)CC)ccc(c4)OC
OpenEye OEToolkits 2.0.6CCN1C(=CN(C1=O)Cc2[nH]c3ccc(nc3n2)Cl)Cc4ccc(cc4Cl)OC
CACTVS 3.385CCN1C(=O)N(Cc2[nH]c3ccc(Cl)nc3n2)C=C1Cc4ccc(OC)cc4Cl
FormulaC20 H19 Cl2 N5 O2
Name1-[(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)methyl]-4-[(2-chloro-4-methoxyphenyl)methyl]-3-ethyl-1,3-dihydro-2H-imidazol-2-one
ChEMBLCHEMBL4757779
DrugBank
ZINC
PDB chain6cml Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6cml Structure-guided discovery of selective methionyl-tRNA synthetase inhibitors with potent activity against Trypanosoma brucei
Resolution2.7 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 G290 V473 A477 Y481 F522
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 G59 V235 A239 Y243 F284
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 S152 S155 K316 K319
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:6cml, PDBe:6cml, PDBj:6cml
PDBsum6cml
PubMed
UniProtQ38C91

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