Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.44 kDa 
• Atom Count: 2534 
• Residue Count: 298 
• Unique protein chains: 1

2B54

Human cyclin dependent kinase 2 (CKD2)complexed with DIN-232305

• DOI: 10.2210/pdb2B54/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-09-27 Released: 2005-10-11 
• Deposition Author(s): Chang, C.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.263 
• R-Value Work: 0.158 

Literature

Synthesis and biological evaluation of 1-aryl-4,5-dihydro-1h-pyraxolo[3,4-d]pyrimidin-4-one inhibitors of cyclin dependent kinases

Markwalder, J.A., Arnone, M.R., Benfield, P.A., Boisclair, M., Burton, C.R., Chang, C.-C., Cox, S.S., Czerniak, P.M., Dean, C.L., Dolenaik, D., Grafstrom, R., Harrison, B.A., Kaltenbach III, R.F., Nugiel, D.A., Rossi, K.A., Sherk, S.R., Sisk, L.M., Stouten, P., Trainor, G.L., Worland, P., Seitz, S.P.

(2004) J Med Chem 47: 5894-5911

• PubMed: 15537345 
• DOI: 10.1021/jm020455u
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Using a high-throughput screening strategy, a series of 1-aryl-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-4-ones was identified that inhibit the cyclin-dependent kinase (CDK) 4/cyclin D1 complex-mediated phosphorylation of a protein substrate with IC(50)s in the low micromolar range. On the basis of preliminary structure-activity relationships (SAR), a model was proposed in which these inhibitors occupy the ATP-binding site of the enzyme, forming critical hydrogen bonds to the same residue (Val96) to which the amino group in ATP is presumed to bind. X-ray diffraction studies on a later derivative bound to CDK2 support this binding mode. Iterative cycles of synthesis and screening lead to a novel series of potent, CDK2-selective 6-(arylmethyl)pyrazolopyrimidinones. Placement of a hydrogen-bond donor in the meta-position on the 6-arylmethyl group resulted in approximately 100-fold increases in CDK4 affinity, giving ligands that were equipotent inhibitors of CDK4 and CDK2. These compounds exhibit antiproliferative effects in the NCI HCT116 and other cell lines. The potency of these antiproliferative effects is enhanced in anilide derivatives and translates into tumor growth inhibition in a mouse xenograft model.

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Organizational Affiliation: 

Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division protein kinase 2	A	298	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens) Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941 GTEx  ENSG00000123374

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D05	A	6-(3,4-DIHYDROXYBENZYL)-3-ETHYL-1-(2,4,6-TRICHLOROPHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4(5H)-ONE C20 H15 Cl3 N4 O3 OPRAIFVPXXVXDL-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
D05	IC50:  20   nM  BindingDB
D05	IC50 :  20   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.263 
• R-Value Work: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.97	α = 90
b = 73.16	β = 90
c = 54.26	γ = 90

Software Package:

Software Name	Purpose
PROCESS	data collection
SCALE	data reduction
X-PLOR	model building
CNX	refinement
PROCESS	data reduction
SCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-27 
• Released Date: 2005-10-11 
Deposition Author(s): Chang, C.-C.

Revision History 

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance