Compound three letter code : 6ZV
 
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Entry Information
Entry status  (1)
REL
(4)
 
Experimental methods  (1)
X-ray diffraction
(4)
 
Authors  (26)
Anand K
(2)
Duster R
(2)
Düster R
(2)
Geyer M
(2)
Gray NS
(2)
Kaltheuner IH
(2)
Moecking J
(2)
Wang J
(2)
Bergqvist S
(1)
Chen P
(1)
Deihl W
(1)
Diehl W
(1)
Ferre RA
(1)
He Y-A
(1)
He YA
(1)
Hilgers MT
(1)
Hu W
(1)
Lam H
(1)
Lee NV
(1)
Murray BW
(1)
Nagata A
(1)
Pelletier LA
(1)
Solowiej J
(1)
VanArsdale T
(1)
Xu M
(1)
Yu X
(1)
 
Homo / hetero assembly  (2)
homo
(3)
hetero
(1)
 
Assembly composition  (2)
protein structure
(3)
protein/protein complex
(1)
 
Assembly polymer count  (2)
monomer
(3)
dimer
(1)
 
Resolution distribution
1.5 - 2
(1)
2.0 - 2.5
(1)
2.5 - 3
(2)
 
Release year distribution
2015 - 2020
(1)
2020 - 2025
(3)
 
Journal  (3)
Nat Commun
(2)
Mol Cancer Ther
(1)
To be published
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(4)
 
Organism name  (1)
Homo sapiens
(4)
 
Molecule name  (19)
ANPK
(1)
Androgen receptor-interacting nuclear protein kinase
(1)
Cell division protein kinase 4
(1)
Cell division protein kinase 6
(1)
Cyclin-dependent kinase 4
(1)
Cyclin-dependent kinase 6
(1)
Dual specificity YAK1-related kinase
(1)
Dual specificity tyrosine-phosphorylation-regulated kinase 1A
(1)
FIST
(1)
Fas-interacting serine/threonine-protein kinase
(1)
G1/S-specific cyclin-D3
(1)
HP86
(1)
Homeodomain-interacting protein kinase 3
(1)
Homolog of protein kinase YAK1
(1)
MNBH
(1)
PSK-J3
(1)
Protein kinase minibrain homolog
(1)
Serine/threonine-protein kinase PLSTIRE
(1)
hMNB
(1)
 
Molecule type  (1)
Protein
(4)
 
Gene names  (12)
CCND3
(1)
CDK4
(1)
CDK6
(1)
CDKN6
(1)
DYRK
(1)
DYRK1A
(1)
DYRK6
(1)
FIST3
(1)
HIPK3
(1)
MNB
(1)
MNBH
(1)
PKY
(1)
 
Interacting Molecules  (2)
Cyclin-dependent kinase 4
(1)
G1/S-specific cyclin-D3
(1)
 
Interacting ligands  (4)
6ZV : N-{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
(4)
EDO : 1,2-ETHANEDIOL
(1)
FLC : CITRATE ANION
(1)
PEG : DI(HYDROXYETHYL)ETHER
(1)
 
Function and Biology
EC number / name  (4)
2.7.11.22 : Cyclin-dependent kinase
(2)
2.7.11.1 : Non-specific serine/threonine protein kinase
(1)
2.7.11.23 : [RNA-polymerase]-subunit kinase
(1)
2.7.12.1 : Dual-specificity kinase
(1)
 
Biological function  (13)
ATP binding
(4)
protein kinase activity
(4)
cyclin binding
(2)
cyclin-dependent protein serine/threonine kinase activity
(2)
kinase activity
(2)
nucleotide binding
(2)
protein binding
(2)
protein serine kinase activity
(2)
protein serine/threonine kinase activity
(2)
transferase activity
(2)
FBXO family protein binding
(1)
cyclin-dependent protein serine/threonine kinase regulator activity
(1)
protein serine/threonine/tyrosine kinase activity
(1)
 
Biological process  (48)
protein phosphorylation
(4)
G1/S transition of mitotic cell cycle
(2)
cell division
(2)
positive regulation of fibroblast proliferation
(2)
regulation of G2/M transition of mitotic cell cycle
(2)
regulation of cell cycle
(2)
regulation of gene expression
(2)
signal transduction
(2)
DNA damage response
(1)
Notch signaling pathway
(1)
T cell differentiation in thymus
(1)
astrocyte development
(1)
cell dedifferentiation
(1)
cell differentiation
(1)
cellular response to interleukin-4
(1)
cellular response to ionomycin
(1)
cellular response to lipopolysaccharide
(1)
cellular response to phorbol 13-acetate 12-myristate
(1)
dentate gyrus development
(1)
generation of neurons
(1)
gliogenesis
(1)
hematopoietic progenitor cell differentiation
(1)
hematopoietic stem cell differentiation
(1)
hemopoiesis
(1)
lateral ventricle development
(1)
negative regulation of cell cycle
(1)
negative regulation of cell differentiation
(1)
negative regulation of cell population proliferation
(1)
negative regulation of cellular senescence
(1)
negative regulation of epithelial cell proliferation
(1)
negative regulation of monocyte differentiation
(1)
negative regulation of myeloid cell differentiation
(1)
negative regulation of osteoblast differentiation
(1)
negative regulation of transcription by RNA polymerase II
(1)
positive regulation of G2/M transition of mitotic cell cycle
(1)
positive regulation of cell population proliferation
(1)
positive regulation of cell-matrix adhesion
(1)
positive regulation of gene expression
(1)
protein autophosphorylation
(1)
regulation of cell motility
(1)
regulation of cell population proliferation
(1)
regulation of erythrocyte differentiation
(1)
regulation of hematopoietic stem cell differentiation
(1)
regulation of transcription initiation by RNA polymerase II
(1)
regulation of type B pancreatic cell proliferation
(1)
response to virus
(1)
response to xenobiotic stimulus
(1)
type B pancreatic cell development
(1)
 
Biological cell component  (21)
cyclin-dependent protein kinase holoenzyme complex
(2)
cytoplasm
(2)
cytosol
(2)
nucleoplasm
(2)
nucleus
(2)
bicellular tight junction
(1)
cell projection
(1)
centrosome
(1)
chromatin
(1)
cyclin D1-CDK4 complex
(1)
cyclin D1-CDK6 complex
(1)
cyclin D2-CDK4 complex
(1)
cyclin D2-CDK6 complex
(1)
cyclin D3-CDK4 complex
(1)
cyclin D3-CDK6 complex
(1)
cytoskeleton
(1)
membrane
(1)
nuclear membrane
(1)
nucleolus
(1)
ruffle
(1)
transcription regulator complex
(1)
 
Sequence and Structure classification
CATH class  (2)
Alpha Beta
(1)
Mainly Alpha
(1)
 
CATH topology  (2)
Phosphorylase Kinase; domain 1
(1)
Transferase(Phosphotransferase); domain 1
(1)
 
Pfam accession / name  (3)
PF00069 : Pkinase
(4)
PF00134 : Cyclin_N
(1)
PF02984 : Cyclin_C
(1)
 
Experimental Information
Diffraction protocol  (1)
Single wavelength
(4)
 
Diffraction radiation source type  (1)
Synchrotron
(4)
 
Diffraction source  (3)
SLS BEAMLINE X06SA
(2)
APS BEAMLINE 17-ID
(1)
APS BEAMLINE 31-ID
(1)
 
Synchrotron site  (2)
APS
(2)
SLS
(2)
 
Diffraction detector type  (1)
Pixel
(4)
 
Refinement software  (2)
PHENIX
(3)
BUSTER
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 4 of 4
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The X-ray co-crystal structure of human CDK6 and Abemaciclib.
Chen P, Ferre RA, Deihl W, Yu X, He Y-A
Mol Cancer Ther (2016) [PMID: 27496135  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: 6ZV    6ZV   
Assembly name: Cyclin-dependent kinase 6 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169439 (Preferred)   search this ID
PDBe-KB: Q00534   
X-ray diffraction
2.27Å resolution
Released: 24 Aug 2016
Model geometry
Fit model/data
5l2s
5l2s
5l2s
Crystal structure of the human DYRK1A kinase domain bound to abemaciclib
Kaltheuner IH, Anand K, Geyer M
Nat Commun (2021) [PMID: 34785661  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: 6ZV    LI    PEG    PEG    LI    FLC    6ZV    EDO   
Modified residues: PTR    PTR   
Assembly name: Dual specificity tyrosine-phosphorylation-regulated kinase 1A (Preferred)   search this complex
PDBe complex ID: PDB-CPX-171789 (Preferred)   search this ID
PDBe-KB: Q13627   
X-ray diffraction
1.82Å resolution
Released: 24 Nov 2021
Model geometry
Fit model/data
7o7k
7o7k
7o7k
Crystal structure of the human HIPK3 kinase domain bound to abemaciclib
Kaltheuner IH, Anand K, Geyer M
Nat Commun (2021) [PMID: 34785661  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: 6ZV    6ZV   
Modified residues: PTR    PTR   
Assembly name: Homeodomain-interacting protein kinase 3 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-190595 (Preferred)   search this ID
PDBe-KB: Q9H422   
X-ray diffraction
2.81Å resolution
Released: 24 Nov 2021
Model geometry
Fit model/data
7o7j
7o7j
7o7j
Structure of CDK4-Cyclin D3 bound to abemaciclib
Hilgers MT, Pelletier LA
To be published
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: 6ZV    6ZV   
Modified residues: ACE    TPO    ACE    TPO   
Assembly name: Cyclin D3-CDK4 complex (Preferred)   search this complex
PDBe complex ID: PDB-CPX-145932 (Preferred)   search this ID
PDBe-KB: P11802    P30281   
X-ray diffraction
2.51Å resolution
Released: 2 Nov 2022
Model geometry
Fit model/data
7sj3
7sj3
7sj3
Entries 1 to 4 of 4
Entries 1 to 4 of 4