Structure of PDB 5l2s Chain A Binding Site BS01

Receptor Information
>5l2s Chain A (length=263) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVPLSTIREVAVLRH
LETFEHPNVVRLFDVCTKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDM
MFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLAVTLWYRAP
EVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLP
GEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKR
ISAYSALSHPYFQ
Ligand information
Ligand ID6ZV
InChIInChI=1S/C27H32F2N8/c1-5-35-8-10-36(11-9-35)16-19-6-7-24(30-14-19)33-27-31-15-22(29)25(34-27)20-12-21(28)26-23(13-20)37(17(2)3)18(4)32-26/h6-7,12-15,17H,5,8-11,16H2,1-4H3,(H,30,31,33,34)
InChIKeyUZWDCWONPYILKI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCN1CCN(CC1)Cc2ccc(Nc3ncc(F)c(n3)c4cc(F)c5nc(C)n(C(C)C)c5c4)nc2
ACDLabs 12.01C(C)N1CCN(CC1)Cc5ccc(Nc2nc(c(F)cn2)c4cc3c(nc(C)n3C(C)C)c(c4)F)nc5
OpenEye OEToolkits 2.0.5CCN1CCN(CC1)Cc2ccc(nc2)Nc3ncc(c(n3)c4cc5c(c(c4)F)nc(n5C(C)C)C)F
FormulaC27 H32 F2 N8
NameN-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine;
Abemaciclib
ChEMBLCHEMBL3301610
DrugBankDB12001
ZINCZINC000072318121
PDB chain5l2s 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5l2s Spectrum and Degree of CDK Drug Interactions Predicts Clinical Performance.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		I19 Y24 A41 K43 F98 V101 D104 L152 D163
Binding residue
(residue number reindexed from 1)		I9 Y14 A31 K33 F73 V76 D79 L127 D138
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.08,Kd=83nM
BindingDB: IC50=10.0nM,Ki=8.2nM
Enzymatic activity
Catalytic site (original residue number in PDB) D145 K147 Q149 N150 D163 T182
Catalytic site (residue number reindexed from 1) D120 K122 Q124 N125 D138 T144
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5l2s, PDBe:5l2s, PDBj:5l2s
PDBsum5l2s
PubMed27496135
UniProtQ00534|CDK6_HUMAN Cyclin-dependent kinase 6 (Gene Name=CDK6)

[Back to BioLiP]