Structure of PDB 5j5a Chain B Binding Site BS01

Receptor Information
>5j5a Chain B (length=523) 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
TTNEQHKAVVKELWTKLEQKGDIYLGRYEGWYSISDEFLTPQNKVSLESG
HVVTWVSEENYMFRLSAFRERLLEWYHANPGCIVPEFRRREVIRAVEKGL
PDLSVSRARATLHNWAIPVPGNPDHCVYVWLDALTNYLTGSRLRVDESGK
EVSLVDDFNELERFPADVHVIGKDILKFHAIYWPAFLLSAGLPLPKKIVA
HGWWTKDRKKISKSLGNVFDPVEKAEEFGYDALKYFLLRESGFSDDGDYS
DKNMIARLNGELADTLGNLVMRCTSAKINVNGEWPSPAAYTEEDESLIQL
IKDLPGTADHYYLIPDIQKAIIAVFDVLRAINAYVTDMAPWKLVKTDPER
LRTVLYITLEGVRVTTLLLSPILPRKSVVIFDMLGVPEVHRKGIENFEFG
AVPPGTRLGPAVEGEVLFSKRST
Ligand information
Ligand ID756
InChIInChI=1S/C22H21N3O2/c1-14-11-17-12-15(8-9-20(17)27-14)22(26)25-10-4-5-16(13-25)21-23-18-6-2-3-7-19(18)24-21/h2-3,6-9,11-12,16H,4-5,10,13H2,1H3,(H,23,24)/t16-/m0/s1
InChIKeyPWUXNVBUFJIXEG-INIZCTEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4Cc1cc2cc(ccc2o1)C(=O)N3CCC[C@@H](C3)c4[nH]c5ccccc5n4
CACTVS 3.385Cc1oc2ccc(cc2c1)C(=O)N3CCC[CH](C3)c4[nH]c5ccccc5n4
CACTVS 3.385Cc1oc2ccc(cc2c1)C(=O)N3CCC[C@@H](C3)c4[nH]c5ccccc5n4
ACDLabs 12.01O=C(c1ccc2oc(cc2c1)C)N3CC(CCC3)c4nc5c(n4)cccc5
OpenEye OEToolkits 2.0.4Cc1cc2cc(ccc2o1)C(=O)N3CCCC(C3)c4[nH]c5ccccc5n4
FormulaC22 H21 N3 O2
Name[(3S)-3-(1H-benzimidazol-2-yl)piperidin-1-yl](2-methyl-1-benzofuran-5-yl)methanone;
2-[1-(2-methyl-1-benzofuran-5-carbonyl)piperidin-3-yl]-1H-1,3-benzodiazole
ChEMBL
DrugBank
ZINCZINC000072481333
PDB chain5j5a 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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PDB5j5a Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		I248 Y250 D287 H289 G290 V473 Y481 F522 H523
Binding residue
(residue number reindexed from 1)		I17 Y19 D56 H58 G59 V229 Y237 F278 H279
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 S146 S149 K310 K313
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:5j5a, PDBe:5j5a, PDBj:5j5a
PDBsum5j5a
PubMed27788467
UniProtQ38C91

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