Structure of PDB 5hne Chain B Binding Site BS02

Receptor Information
>5hne Chain B (length=358) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSFKAADLQLEMTQKPHKKPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQ
NLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRL
CLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQ
PTRALLFVILCPVGAYFPGGSVTPVSLLADPAFIRAWVGGVGNYKLGGNY
GPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELV
TPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVRE
VFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIR
AHEWMFPV
Ligand information
Ligand IDEL2
InChIInChI=1S/C25H24BrN5O2S/c1-27-24(32)15-8-9-20-19(13-15)30-23(18-7-2-3-12-28-18)31(20)17-6-4-5-16(14-17)29-25(33)21-10-11-22(26)34-21/h2-3,7-13,16-17H,4-6,14H2,1H3,(H,27,32)(H,29,33)/t16-,17+/m0/s1
InChIKeyPGSKODUPOMCUEJ-DLBZAZTESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)c1ccc2n([CH]3CCC[CH](C3)NC(=O)c4sc(Br)cc4)c(nc2c1)c5ccccn5
OpenEye OEToolkits 2.0.4CNC(=O)c1ccc2c(c1)nc(n2[C@@H]3CCC[C@@H](C3)NC(=O)c4ccc(s4)Br)c5ccccn5
OpenEye OEToolkits 2.0.4CNC(=O)c1ccc2c(c1)nc(n2C3CCCC(C3)NC(=O)c4ccc(s4)Br)c5ccccn5
CACTVS 3.385CNC(=O)c1ccc2n([C@@H]3CCC[C@@H](C3)NC(=O)c4sc(Br)cc4)c(nc2c1)c5ccccn5
ACDLabs 12.01CNC(c4ccc3n(C1CCCC(C1)NC(=O)c2ccc(s2)Br)c(nc3c4)c5ccccn5)=O
FormulaC25 H24 Br N5 O2 S
Name1-[(1R,3S)-3-{[(5-bromothiophen-2-yl)carbonyl]amino}cyclohexyl]-N-methyl-2-(pyridin-2-yl)-1H-benzimidazole-5-carboxamide
ChEMBLCHEMBL3808902
DrugBank
ZINCZINC000584905544
PDB chain5hne Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5hne Discovery and Optimization of Potent, Selective, and in Vivo Efficacious 2-Aryl Benzimidazole BCATm Inhibitors.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		F30 F75 K79 Q224 V238 G239 T240 M241 A314 C318
Binding residue
(residue number reindexed from 1)		F23 F68 K72 Q217 V231 G232 T233 M234 A307 C311
Annotation score1
Binding affinityMOAD: ic50=50nM
BindingDB: IC50=100nM
Enzymatic activity
Catalytic site (original residue number in PDB) K202
Catalytic site (residue number reindexed from 1) K195
Enzyme Commision number 2.6.1.42: branched-chain-amino-acid transaminase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004084 branched-chain-amino-acid transaminase activity
GO:0005515 protein binding
GO:0008483 transaminase activity
GO:0052654 L-leucine-2-oxoglutarate transaminase activity
GO:0052655 L-valine-2-oxoglutarate transaminase activity
GO:0052656 L-isoleucine-2-oxoglutarate transaminase activity
Biological Process
GO:0006549 isoleucine metabolic process
GO:0006550 isoleucine catabolic process
GO:0006551 L-leucine metabolic process
GO:0006573 valine metabolic process
GO:0006629 lipid metabolic process
GO:0008652 amino acid biosynthetic process
GO:0009081 branched-chain amino acid metabolic process
GO:0009082 branched-chain amino acid biosynthetic process
GO:0009083 branched-chain amino acid catabolic process
GO:0009098 L-leucine biosynthetic process
GO:0009099 L-valine biosynthetic process
GO:0010817 regulation of hormone levels
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5hne, PDBe:5hne, PDBj:5hne
PDBsum5hne
PubMed27096045
UniProtO15382|BCAT2_HUMAN Branched-chain-amino-acid aminotransferase, mitochondrial (Gene Name=BCAT2)

[Back to BioLiP]