Structure of PDB 4dzy Chain A Binding Site BS01

Receptor Information
>4dzy Chain A (length=309) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLTPTMMLYSGRSQDGSHLLKSGRYLQQELPVRIAHRIKGFRSLPFIIGC
NPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQLLDDHKDVVTL
LAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHHLALHEDKPDFV
GIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGHVAARFPFIPMP
LDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGG
GIAHKDLDRVMDYHFTTAGFGFGLPTSRAYAEYLGGSLQLQSLQGIGTDV
YLRLRHIDG
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 chain4dzy Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dzy Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase.
Resolution2.101 Å
Binding residue
(original residue number in PDB)		N249 R252 A253 I290 V298 T304 T305 G335 G337 G339 L340
Binding residue
(residue number reindexed from 1)		N211 R214 A215 I252 V260 T266 T267 G269 G271 G273 L274
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) Y241 E245 K248 N249
Catalytic site (residue number reindexed from 1) Y203 E207 K210 N211
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4dzy, PDBe:4dzy, PDBj:4dzy
PDBsum4dzy
PubMed23716694
UniProtQ00972|BCKD_RAT Branched-chain alpha-ketoacid dehydrogenase kinase (Gene Name=Bckdk)

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