Structure of PDB 5l2t Chain A Binding Site BS01

Receptor Information
>5l2t Chain A (length=261) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVSTIREVAVLRHLE
TFEHPNVVRLFDVCTKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMF
QLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLAVTLWYRAPEV
LLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGE
EDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRIS
AYSALSHPYFQ
Ligand information
Ligand ID6ZZ
InChIInChI=1S/C23H30N8O/c1-29(2)22(32)19-13-16-14-26-23(28-21(16)31(19)17-5-3-4-6-17)27-20-8-7-18(15-25-20)30-11-9-24-10-12-30/h7-8,13-15,17,24H,3-6,9-12H2,1-2H3,(H,25,26,27,28)
InChIKeyRHXHGRAEPCAFML-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1(nc2c(cn1)cc(C(N(C)C)=O)n2C3CCCC3)Nc4ncc(cc4)N5CCNCC5
OpenEye OEToolkits 2.0.5CN(C)C(=O)c1cc2cnc(nc2n1C3CCCC3)Nc4ccc(cn4)N5CCNCC5
CACTVS 3.385CN(C)C(=O)c1cc2cnc(Nc3ccc(cn3)N4CCNCC4)nc2n1C5CCCC5
FormulaC23 H30 N8 O
Name7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide;
Ribociclib
ChEMBLCHEMBL3545110
DrugBankDB11730
ZINCZINC000072316335
PDB chain5l2t Chain A Residue 900 [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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PDB5l2t Spectrum and Degree of CDK Drug Interactions Predicts Clinical Performance.
Resolution2.37 Å
Binding residue
(original residue number in PDB)		I19 A41 F98 V101 D104 L152 D163
Binding residue
(residue number reindexed from 1)		I9 A31 F71 V74 D77 L125 D136
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.19,Kd=650nM
BindingDB: IC50=39nM
Enzymatic activity
Catalytic site (original residue number in PDB) D145 K147 Q149 N150 D163 T182
Catalytic site (residue number reindexed from 1) D118 K120 Q122 N123 D136 T142
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:0030332 cyclin binding
GO:0098770 FBXO family protein binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001954 positive regulation of cell-matrix adhesion
GO:0002244 hematopoietic progenitor cell differentiation
GO:0003323 type B pancreatic cell development
GO:0006468 protein phosphorylation
GO:0007165 signal transduction
GO:0007219 Notch signaling pathway
GO:0008285 negative regulation of cell population proliferation
GO:0009615 response to virus
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0010468 regulation of gene expression
GO:0010628 positive regulation of gene expression
GO:0014002 astrocyte development
GO:0016310 phosphorylation
GO:0021542 dentate gyrus development
GO:0021670 lateral ventricle development
GO:0030097 hemopoiesis
GO:0030154 cell differentiation
GO:0033077 T cell differentiation in thymus
GO:0042063 gliogenesis
GO:0042127 regulation of cell population proliferation
GO:0043697 cell dedifferentiation
GO:0045596 negative regulation of cell differentiation
GO:0045638 negative regulation of myeloid cell differentiation
GO:0045646 regulation of erythrocyte differentiation
GO:0045656 negative regulation of monocyte differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0045786 negative regulation of cell cycle
GO:0048146 positive regulation of fibroblast proliferation
GO:0048699 generation of neurons
GO:0050680 negative regulation of epithelial cell proliferation
GO:0051301 cell division
GO:0051726 regulation of cell cycle
GO:0060218 hematopoietic stem cell differentiation
GO:1902036 regulation of hematopoietic stem cell differentiation
GO:2000145 regulation of cell motility
GO:2000773 negative regulation of cellular senescence
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0001726 ruffle
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0042995 cell projection
GO:0097131 cyclin D1-CDK6 complex
GO:0097132 cyclin D2-CDK6 complex
GO:0097133 cyclin D3-CDK6 complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5l2t, PDBe:5l2t, PDBj:5l2t
PDBsum5l2t
PubMed27496135
UniProtQ00534|CDK6_HUMAN Cyclin-dependent kinase 6 (Gene Name=CDK6)

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