Structure of PDB 3d2r Chain A Binding Site BS01

Receptor Information
>3d2r Chain A (length=354) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PREVEHFSRYSPSPLSMKQLLDFGSENCERTSFAFLRQELPVRLANILKE
IDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLI
KVRNRHHNVVPTMAQGIIEYKDACDPVTNQNLQYFLDRFYMNRISTRMLM
NQHILIFSDSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQ
VNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVI
VVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTAPLAGFGYGLPIS
RLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHYD
DWCI
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3d2r Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3d2r Pyruvate Dehydrogenase Kinase-4 Structures Reveal a Metastable Open Conformation Fostering Robust Core-free Basal Activity.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		N258 A262 V298 L306 S312 T313 A328 G331 L334
Binding residue
(residue number reindexed from 1)		N229 A233 V269 L277 S283 T284 A291 G294 L297
Annotation score5
Binding affinityMOAD: Kd=3.3uM
PDBbind-CN: -logKd/Ki=5.48,Kd=3.3uM
Enzymatic activity
Catalytic site (original residue number in PDB) H250 E254 K257 N258
Catalytic site (residue number reindexed from 1) H221 E225 K228 N229
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3d2r, PDBe:3d2r, PDBj:3d2r
PDBsum3d2r
PubMed18658136
UniProtQ16654|PDK4_HUMAN [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial (Gene Name=PDK4)

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