Structure of PDB 6p8e Chain B Binding Site BS02

Receptor Information
>6p8e Chain B (length=260) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GTVYKARDPHSGHFVALKSVRVPNGEEGLPISTVREVALLRRLEAFEHPN
VVRLMDVCATSEIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQF
LRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLTLWYRAPEVLLQS
TYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWP
RDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRA
LQHSYLHKDE
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6p8e Chain B Residue 402 [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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PDB6p8e p27 allosterically activates cyclin-dependent kinase 4 and antagonizes palbociclib inhibition.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G42 E44 G45
Binding residue
(residue number reindexed from 1)		G25 E27 G28
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D137 K139 E141 N142 D155 T174
Catalytic site (residue number reindexed from 1) D116 K118 E120 N121 D134 T138
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004693 cyclin-dependent protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
GO:0030332 cyclin binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0006468 protein phosphorylation
GO:0007165 signal transduction
GO:0008284 positive regulation of cell population proliferation
GO:0009410 response to xenobiotic stimulus
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0010468 regulation of gene expression
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0016310 phosphorylation
GO:0048146 positive regulation of fibroblast proliferation
GO:0051301 cell division
GO:0051726 regulation of cell cycle
GO:0060260 regulation of transcription initiation by RNA polymerase II
GO:0061469 regulation of type B pancreatic cell proliferation
GO:0071222 cellular response to lipopolysaccharide
GO:0071353 cellular response to interleukin-4
GO:1904628 cellular response to phorbol 13-acetate 12-myristate
GO:1904637 cellular response to ionomycin
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005923 bicellular tight junction
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0097128 cyclin D1-CDK4 complex
GO:0097129 cyclin D2-CDK4 complex
GO:0097130 cyclin D3-CDK4 complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6p8e, PDBe:6p8e, PDBj:6p8e
PDBsum6p8e
PubMed31831640
UniProtP11802|CDK4_HUMAN Cyclin-dependent kinase 4 (Gene Name=CDK4)

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