Structure of PDB 5j58 Chain B Binding Site BS01

Receptor Information
>5j58 Chain B (length=531) 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
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGNP
CKVSLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREV
IRAVEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSR
LRVDESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGL
PLPKKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESG
FSDDGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTE
EDESLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWK
LVKTDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRK
GIENFEFGAVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand IDN56
InChIInChI=1S/C18H18Cl3N5/c19-12-6-11(7-13(20)8-12)9-22-14-2-1-5-26(10-14)18-23-15-3-4-16(21)24-17(15)25-18/h3-4,6-8,14,22H,1-2,5,9-10H2,(H,23,24,25)/t14-/m0/s1
InChIKeyALKJREGOUJGYEK-AWEZNQCLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1cc(nc2c1[nH]c(n2)N3CCC[C@@H](C3)NCc4cc(cc(c4)Cl)Cl)Cl
ACDLabs 12.01Clc1cc(Cl)cc(c1)CNC2CCCN(C2)c3nc4c(n3)nc(cc4)Cl
CACTVS 3.385Clc1cc(Cl)cc(CN[C@H]2CCCN(C2)c3[nH]c4ccc(Cl)nc4n3)c1
OpenEye OEToolkits 2.0.4c1cc(nc2c1[nH]c(n2)N3CCCC(C3)NCc4cc(cc(c4)Cl)Cl)Cl
CACTVS 3.385Clc1cc(Cl)cc(CN[CH]2CCCN(C2)c3[nH]c4ccc(Cl)nc4n3)c1
FormulaC18 H18 Cl3 N5
Name(3S)-1-(5-chloro-1H-imidazo[4,5-b]pyridin-2-yl)-N-[(3,5-dichlorophenyl)methyl]piperidin-3-amine
ChEMBLCHEMBL3953659
DrugBank
ZINCZINC000584905777
PDB chain5j58 Chain B Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5j58 Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Y250 D287 G290 V473 W474 F522 H523
Binding residue
(residue number reindexed from 1)		Y19 D56 G59 V237 W238 F286 H287
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.30,IC50<50nM
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 S154 S157 K318 K321
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:5j58, PDBe:5j58, PDBj:5j58
PDBsum5j58
PubMed27788467
UniProtQ38C91

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