Structure of PDB 6gu6 Chain A Binding Site BS01

Receptor Information
>6gu6 Chain A (length=288) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIR
EISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYM
DSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLA
RAFGIPITHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPL
FHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHV
KNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLD
Ligand information
Ligand ID1QK
InChIInChI=1S/C21H29N6O2/c1-2-17-14-23-27-19(22-13-16-6-5-9-25(29)15-16)12-20(24-21(17)27)26-10-4-3-7-18(26)8-11-28/h5-6,9,12,14-15,18,22,28-29H,2-4,7-8,10-11,13H2,1H3/q+1/t18-/m0/s1
InChIKeyWBUFFOKXERTKGU-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCc1cnn2c(NCc3ccc[n+](O)c3)cc(nc12)N4CCCC[CH]4CCO
OpenEye OEToolkits 1.7.6CCc1cnn2c1nc(cc2NCc3ccc[n+](c3)O)N4CCCCC4CCO
ACDLabs 12.01n2c(cc(NCc1ccc[n+](O)c1)n3ncc(c23)CC)N4C(CCO)CCCC4
OpenEye OEToolkits 1.7.6CCc1cnn2c1nc(cc2NCc3ccc[n+](c3)O)N4CCCC[C@H]4CCO
CACTVS 3.370CCc1cnn2c(NCc3ccc[n+](O)c3)cc(nc12)N4CCCC[C@H]4CCO
FormulaC21 H29 N6 O2
Name3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium;
DINACICLIB
ChEMBL
DrugBank
ZINCZINC000103522275
PDB chain6gu6 Chain A Residue 301 [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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PDB6gu6 Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition.
Resolution2.33 Å
Binding residue
(original residue number in PDB)		G11 E12 A31 K33 F80 L83 S84 M85 D86 Q132 L135
Binding residue
(residue number reindexed from 1)		G11 E12 A31 K33 F80 L83 S84 M85 D86 Q132 L135
Annotation score1
Binding affinityMOAD: Kd=1810nM
PDBbind-CN: -logKd/Ki=5.74,Kd=1810nM
Enzymatic activity
Catalytic site (original residue number in PDB) D128 K130 Q132 N133 D146 T166
Catalytic site (residue number reindexed from 1) D128 K130 Q132 N133 D146 T163
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
2.7.11.23: [RNA-polymerase]-subunit kinase.
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0003682 chromatin binding
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:0008353 RNA polymerase II CTD heptapeptide repeat kinase activity
GO:0016301 kinase activity
GO:0030332 cyclin binding
GO:0030544 Hsp70 protein binding
GO:0035173 histone kinase activity
GO:0097472 cyclin-dependent protein kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000086 G2/M transition of mitotic cell cycle
GO:0000226 microtubule cytoskeleton organization
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006338 chromatin remodeling
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006468 protein phosphorylation
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0007077 mitotic nuclear membrane disassembly
GO:0007095 mitotic G2 DNA damage checkpoint signaling
GO:0007098 centrosome cycle
GO:0007344 pronuclear fusion
GO:0009410 response to xenobiotic stimulus
GO:0009636 response to toxic substance
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0014038 regulation of Schwann cell differentiation
GO:0014070 response to organic cyclic compound
GO:0014075 response to amine
GO:0014823 response to activity
GO:0016310 phosphorylation
GO:0016477 cell migration
GO:0016579 protein deubiquitination
GO:0018105 peptidyl-serine phosphorylation
GO:0018107 peptidyl-threonine phosphorylation
GO:0030261 chromosome condensation
GO:0030855 epithelial cell differentiation
GO:0031100 animal organ regeneration
GO:0034501 protein localization to kinetochore
GO:0042307 positive regulation of protein import into nucleus
GO:0042542 response to hydrogen peroxide
GO:0042752 regulation of circadian rhythm
GO:0043066 negative regulation of apoptotic process
GO:0044772 mitotic cell cycle phase transition
GO:0045471 response to ethanol
GO:0045740 positive regulation of DNA replication
GO:0045931 positive regulation of mitotic cell cycle
GO:0045995 regulation of embryonic development
GO:0046686 response to cadmium ion
GO:0046688 response to copper ion
GO:0046718 symbiont entry into host cell
GO:0048144 fibroblast proliferation
GO:0048511 rhythmic process
GO:0048678 response to axon injury
GO:0051301 cell division
GO:0055015 ventricular cardiac muscle cell development
GO:0060045 positive regulation of cardiac muscle cell proliferation
GO:0062033 positive regulation of mitotic sister chromatid segregation
GO:0065003 protein-containing complex assembly
GO:0070301 cellular response to hydrogen peroxide
GO:0070371 ERK1 and ERK2 cascade
GO:0071407 cellular response to organic cyclic compound
GO:0090166 Golgi disassembly
GO:1900182 positive regulation of protein localization to nucleus
GO:1902423 regulation of attachment of mitotic spindle microtubules to kinetochore
GO:1902850 microtubule cytoskeleton organization involved in mitosis
GO:1905448 positive regulation of mitochondrial ATP synthesis coupled electron transport
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005789 endoplasmic reticulum membrane
GO:0005813 centrosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005876 spindle microtubule
GO:0016020 membrane
GO:0030496 midbody
GO:0070062 extracellular exosome
GO:0072686 mitotic spindle
GO:0097121 cyclin A1-CDK1 complex
GO:0097122 cyclin A2-CDK1 complex
GO:0097125 cyclin B1-CDK1 complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6gu6, PDBe:6gu6, PDBj:6gu6
PDBsum6gu6
PubMed30472117
UniProtP06493|CDK1_HUMAN Cyclin-dependent kinase 1 (Gene Name=CDK1)

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