Structure of PDB 8f5f Chain B Binding Site BS01

Receptor Information
>8f5f Chain B (length=318) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFYNQSAIDAAAEKPSVRLTPTMMLYGSHLLKSARYLQQELPVRIAHRIK
GFRCLPFIIGCNPTILHVHELYIRAFQKLTDFPPIKDQADEAQYCQLVRQ
LLDDHKDVVTLLAEGLRESRKHIEDEKLVRYFLDKTLTSRLGIRMLATHH
LALHEDKPDFVGIICTRLSPKKIIEKWVDFARRLCEHKYGNAPRVRINGH
VAARFPFIPMPLDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDV
DLIIRISDRGGGIAHKDLDRVMDYHFTTAFGFGLPTSRAYAEYLGGSLQL
QSLQGIGTDVYLRLRHID
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 chain8f5f Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8f5f Small molecule branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors with opposing effects on BDK protein levels.
Resolution3.149 Å
Binding residue
(original residue number in PDB)		N249 A253 D285 G289 I290 V298 T304 T305 F336 G337 G339 L340 T364
Binding residue
(residue number reindexed from 1)		N222 A226 D258 G262 I263 V271 T277 T278 F280 G281 G283 L284 T308
Annotation score5
Enzymatic activity
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:0005515 protein binding
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:0008610 lipid biosynthetic process
GO:0009063 amino acid catabolic process
GO:0009083 branched-chain amino acid catabolic process
GO:0010906 regulation of glucose metabolic process
GO:0016310 phosphorylation
GO:0045763 negative regulation of cellular amino acid metabolic process
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:8f5f, PDBe:8f5f, PDBj:8f5f
PDBsum8f5f
PubMed37558654
UniProtO14874|BCKD_HUMAN Branched-chain alpha-ketoacid dehydrogenase kinase (Gene Name=BCKDK)

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