2EUF

X-ray structure of human CDK6-Vcyclin in complex with the inhibitor PD0332991


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Toward understanding the structural basis of cyclin-dependent kinase 6 specific inhibition.

Lu, H.Schulze-Gahmen, U.

(2006) J.Med.Chem. 49: 3826-3831

  • DOI: 10.1021/jm0600388
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cyclin-dependent kinases (CDKs) are key players in cell cycle control, and genetic alterations of CDKs and their regulators have been linked to a variety of cancers. Hence, CDKs are obvious targets for therapeutic intervention in various proliferativ ...

    Cyclin-dependent kinases (CDKs) are key players in cell cycle control, and genetic alterations of CDKs and their regulators have been linked to a variety of cancers. Hence, CDKs are obvious targets for therapeutic intervention in various proliferative diseases, including cancer. To date, drug design efforts have mostly focused on CDK2 because methods for crystallization of its inhibitor complexes have been well established. CDK4 and CDK6, however, may be at least as important as enzymes for cell cycle regulation and could provide alternative treatment options. We describe here two complex structures of human CDK6 with a very specific kinase inhibitor, PD0332991, which is based on a pyrido[2,3-d]pyrimidin-7-one scaffold, and with the less specific aminopurvalanol inhibitor. Analysis of the structures suggests that relatively small conformational differences between CDK2 and CDK6 in the hinge region are contributing to the inhibitor specificity by inducing changes in the inhibitor orientation that lead to sterical clashes in CDK2 but not CDK6. These complex structures provide valuable insights for the future development of CDK-specific inhibitors.


    Organizational Affiliation

    Physical Biosciences Division at Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS3, Berkeley, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
viral Cyclin
A
254Saimiriine herpesvirus 2 (strain 11)Mutation(s): 0 
Gene Names: 72 (ECLF2)
Find proteins for Q01043 (Saimiriine herpesvirus 2 (strain 11))
Go to UniProtKB:  Q01043
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 6
B
308Homo sapiensMutation(s): 0 
Gene Names: CDK6 (CDKN6)
EC: 2.7.11.22
Find proteins for Q00534 (Homo sapiens)
Go to Gene View: CDK6
Go to UniProtKB:  Q00534
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LQQ
Query on LQQ

Download SDF File 
Download CCD File 
B
6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE
Palbociclib
C24 H29 N7 O2
AHJRHEGDXFFMBM-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LQQIC50: 16 nM (100) BINDINGDB
LQQIC50: 15 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.229 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.146α = 90.00
b = 71.146β = 90.00
c = 446.876γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
AMoREphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance