Structure of PDB 3tz4 Chain A Binding Site BS02

Receptor Information
>3tz4 Chain A (length=310) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIG
CNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVT
LLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDF
VGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPM
PLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRG
GGIAHKDLDRVMDYHFTTAGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTD
VYLRLRHIDG
Ligand information
Ligand ID03H
InChIInChI=1S/C6H11ClO2/c1-4(2)3-5(7)6(8)9/h4-5H,3H2,1-2H3,(H,8,9)/t5-/m0/s1
InChIKeyCBQBIPRPIHIKPW-YFKPBYRVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(C)C[C@@H](C(=O)O)Cl
OpenEye OEToolkits 1.7.2CC(C)CC(C(=O)O)Cl
CACTVS 3.370CC(C)C[CH](Cl)C(O)=O
CACTVS 3.370CC(C)C[C@H](Cl)C(O)=O
ACDLabs 12.01ClC(C(=O)O)CC(C)C
FormulaC6 H11 Cl O2
Name(2S)-2-chloro-4-methylpentanoic acid;
(S)-alpha-chloroisocaproate
ChEMBL
DrugBank
ZINCZINC000002507430
PDB chain3tz4 Chain A Residue 390 [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]
PDB3tz4 Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		I72 Y99 H132 R167 I170 R171
Binding residue
(residue number reindexed from 1)		I35 Y62 H95 R130 I133 R134
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.49,Kd=3.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y241 E245 K248 N249
Catalytic site (residue number reindexed from 1) Y204 E208 K211 N212
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
2.7.11.4: [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004722 protein serine/threonine phosphatase activity
GO:0004740 pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0047323 [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0006550 isoleucine catabolic process
GO:0006552 L-leucine catabolic process
GO:0006574 valine catabolic process
GO:0007283 spermatogenesis
GO:0008610 lipid biosynthetic process
GO:0009083 branched-chain amino acid catabolic process
GO:0010906 regulation of glucose metabolic process
GO:0016310 phosphorylation
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0045252 oxoglutarate dehydrogenase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3tz4, PDBe:3tz4, PDBj:3tz4
PDBsum3tz4
PubMed23716694
UniProtQ00972|BCKD_RAT Branched-chain alpha-ketoacid dehydrogenase kinase (Gene Name=Bckdk)

[Back to BioLiP]