Structure of PDB 2zdy Chain B Binding Site BS02
Receptor Information
>2zdy Chain B (length=354) Species:
9606
(Homo sapiens) [
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PREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILK
EIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTL
IKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTR
MLMNQHILIFSTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSP
ELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSL
TPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTGFGYGLPISR
LYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHYDD
WCIP
Ligand information
Ligand ID
ADP
InChI
InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Formula
C10 H15 N5 O10 P2
Name
ADENOSINE-5'-DIPHOSPHATE
ChEMBL
CHEMBL14830
DrugBank
DB16833
ZINC
ZINC000012360703
PDB chain
2zdy Chain B Residue 1501 [
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Receptor-Ligand Complex Structure
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PDB
2zdy
Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.
Resolution
2.4 Å
Binding residue
(original residue number in PDB)
N258 R261 A262 V298 L306 S312 T313 G329 F330 G331 G333 L334 T358
Binding residue
(residue number reindexed from 1)
N235 R238 A239 V275 L283 S289 T290 G291 F292 G293 G295 L296 T320
Annotation score
5
Enzymatic activity
Catalytic site (original residue number in PDB)
H250 E254 K257 N258
Catalytic site (residue number reindexed from 1)
H227 E231 K234 N235
Enzyme Commision number
2.7.11.2
: [pyruvate dehydrogenase (acetyl-transferring)] kinase.
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
Biological Process
GO:0006885
regulation of pH
GO:0008286
insulin receptor signaling pathway
GO:0009267
cellular response to starvation
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:0042304
regulation of fatty acid biosynthetic process
GO:0042593
glucose homeostasis
GO:0042594
response to starvation
GO:0045124
regulation of bone resorption
GO:0046320
regulation of fatty acid oxidation
GO:0071398
cellular response to fatty acid
GO:0072593
reactive oxygen species metabolic process
GO:2000811
negative regulation of anoikis
Cellular Component
GO:0005739
mitochondrion
GO:0005759
mitochondrial matrix
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:2zdy
,
PDBe:2zdy
,
PDBj:2zdy
PDBsum
2zdy
PubMed
21904029
UniProt
Q16654
|PDK4_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (Gene Name=PDK4)
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