Structure of PDB 5m4m Chain A

Receptor sequence
>5m4mA (length=344) Species: 9606 (Homo sapiens) [Search protein sequence]
GSAPKYIEHFSKFSPSPLSMKQFLDFGSNACEKTSFTFLRQELPVRLANI
MKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTD
ALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRIS
IRMLINQHTLIFDPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPD
LEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILP
PIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPPLAGFGYGL
PISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVY
3D structure
PDB5m4m Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase.
ChainA
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) H239 E243 K246 N247
Catalytic site (residue number reindexed from 1) H226 E230 K233 N234
Enzyme Commision number 2.7.11.2: [pyruvate dehydrogenase (acetyl-transferring)] kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 7FW A N247 R250 A251 D282 G284 V287 L295 S301 A316 G317 F318 G319 T346 N234 R237 A238 D269 G271 V274 L282 S288 A294 G295 F296 G297 T324 MOAD: Ki=1.02uM
BS02 TF3 A L63 P64 R66 V67 G125 V126 Y129 N142 I143 L147 L57 P58 R60 V61 G119 V120 Y123 N136 I137 L141 BindingDB: IC50=2000nM
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004740 pyruvate dehydrogenase (acetyl-transferring) kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006006 glucose metabolic process
GO:0006111 regulation of gluconeogenesis
GO:0006885 regulation of pH
GO:0008286 insulin receptor signaling pathway
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0010565 regulation of cellular ketone metabolic process
GO:0010906 regulation of glucose metabolic process
GO:0016310 phosphorylation
GO:0031670 cellular response to nutrient
GO:0034614 cellular response to reactive oxygen species
GO:0042593 glucose homeostasis
GO:0050848 regulation of calcium-mediated signaling
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0045254 pyruvate dehydrogenase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m4m, PDBe:5m4m, PDBj:5m4m
PDBsum5m4m
PubMed28199108
UniProtQ15119|PDK2_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (Gene Name=PDK2)

[Back to BioLiP]