Structure of PDB 4kd1 Chain A Binding Site BS01

Receptor Information
>4kd1 Chain A (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIR
EISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIP
LPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLAR
AFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRR
ALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSK
VVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
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 chain4kd1 Chain A Residue 302 [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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PDB4kd1 Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		I10 A31 K33 F80 F82 L83 H84 Q85 D86 K89 Q131 L134
Binding residue
(residue number reindexed from 1)		I10 A31 K33 F80 F82 L83 H84 Q85 D86 K89 Q131 L134
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D127 K129 Q131 N132 D145 T158 T165
Catalytic site (residue number reindexed from 1) D127 K129 Q131 N132 D145 T158 T165
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion 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:0016301 kinase activity
GO:0019904 protein domain specific binding
GO:0030332 cyclin binding
GO:0035173 histone kinase activity
GO:0046872 metal ion binding
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:0000122 negative regulation of transcription by RNA polymerase II
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006338 chromatin remodeling
GO:0006351 DNA-templated transcription
GO:0006468 protein phosphorylation
GO:0006813 potassium ion transport
GO:0007099 centriole replication
GO:0007165 signal transduction
GO:0007265 Ras protein signal transduction
GO:0007346 regulation of mitotic cell cycle
GO:0008284 positive regulation of cell population proliferation
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0010468 regulation of gene expression
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0031453 positive regulation of heterochromatin formation
GO:0031571 mitotic G1 DNA damage checkpoint signaling
GO:0032298 positive regulation of DNA-templated DNA replication initiation
GO:0043247 telomere maintenance in response to DNA damage
GO:0043687 post-translational protein modification
GO:0045740 positive regulation of DNA replication
GO:0045893 positive regulation of DNA-templated transcription
GO:0051298 centrosome duplication
GO:0051301 cell division
GO:0051321 meiotic cell cycle
GO:0071732 cellular response to nitric oxide
GO:0090398 cellular senescence
GO:1905784 regulation of anaphase-promoting complex-dependent catabolic process
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0000781 chromosome, telomeric region
GO:0000793 condensed chromosome
GO:0000805 X chromosome
GO:0000806 Y chromosome
GO:0001673 male germ cell nucleus
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0015030 Cajal body
GO:0097123 cyclin A1-CDK2 complex
GO:0097124 cyclin A2-CDK2 complex
GO:0097134 cyclin E1-CDK2 complex
GO:0097135 cyclin E2-CDK2 complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4kd1, PDBe:4kd1, PDBj:4kd1
PDBsum4kd1
PubMed24007471
UniProtP24941|CDK2_HUMAN Cyclin-dependent kinase 2 (Gene Name=CDK2)

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