Structure of PDB 4zt6 Chain B Binding Site BS01

Receptor Information
>4zt6 Chain B (length=528) 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
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDESFLTPQNITDGKV
SLESGHVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRA
VEKGLPDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLRV
DESGKEVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLP
KKIVAHGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSD
DGDYSDKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDE
SLIQLIKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVK
TDPERLRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIE
NFEFGAVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand ID4RD
InChIInChI=1S/C18H18Cl2FN5O/c19-10-8-11-13(4-7-27-16(11)12(20)9-10)22-5-1-6-23-18-24-14-2-3-15(21)25-17(14)26-18/h2-3,8-9,13,22H,1,4-7H2,(H2,23,24,25,26)/t13-/m1/s1
InChIKeyYWDBMYZFLWAEHC-CYBMUJFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1ccc2[nH]c(NCCCN[CH]3CCOc4c(Cl)cc(Cl)cc34)nc2n1
CACTVS 3.385Fc1ccc2[nH]c(NCCCN[C@@H]3CCOc4c(Cl)cc(Cl)cc34)nc2n1
OpenEye OEToolkits 1.9.2c1cc(nc2c1[nH]c(n2)NCCCNC3CCOc4c3cc(cc4Cl)Cl)F
OpenEye OEToolkits 1.9.2c1cc(nc2c1[nH]c(n2)NCCCN[C@@H]3CCOc4c3cc(cc4Cl)Cl)F
ACDLabs 12.01c2cc1nc(nc1nc2F)NCCCNC3CCOc4c3cc(Cl)cc4Cl
FormulaC18 H18 Cl2 F N5 O
NameN-[(4R)-6,8-dichloro-3,4-dihydro-2H-chromen-4-yl]-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine
ChEMBL
DrugBank
ZINCZINC000584905059
PDB chain4zt6 Chain B Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4zt6 5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		P247 I248 Y250 D287 H289 G290 L456 Y472 V473 W474 I519 F522 H523
Binding residue
(residue number reindexed from 1)		P16 I17 Y19 D56 H58 G59 L217 Y233 V234 W235 I280 F283 H284
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 S151 S154 K315 K318
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:4zt6, PDBe:4zt6, PDBj:4zt6
PDBsum4zt6
PubMed27627628
UniProtQ38C91

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