Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2591 
• Residue Count: 292 
• Unique protein chains: 1

2R3O

Crystal Structure of Cyclin-Dependent Kinase 2 with inhibitor

• DOI: 10.2210/pdb2R3O/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2007-08-29 Released: 2008-01-22 
• Deposition Author(s): Fischmann, T.O., Hruza, A.W., Madison, V.M., Duca, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structure-guided discovery of cyclin-dependent kinase inhibitors.

Fischmann, T.O., Hruza, A., Duca, J.S., Ramanathan, L., Mayhood, T., Windsor, W.T., Le, H.V., Guzi, T.J., Dwyer, M.P., Paruch, K., Doll, R.J., Lees, E., Parry, D., Seghezzi, W., Madison, V.

(2008) Biopolymers 89: 372-379

• PubMed: 17937404 
• DOI: 10.1002/bip.20868
• Primary Citation of Related Structures:  
  2R3J, 2R3I, 2R3H, 2R3G, 2R3F, 2R3R, 2R3Q, 2R3P, 2R3O, 2R3N


• PubMed Abstract: 
  

CDK2 inhibitors containing the related bicyclic heterocycles pyrazolopyrimidines and imidazopyrazines were discovered through high-throughput screening. Crystal structures of inhibitors with these bicyclic cores and two more related ones show that all but one have a common binding mode featuring two hydrogen bonds (H-bonds) to the backbone of the kinase hinge region. Even though ab initio computations indicated that the imidazopyrazine core would bind more tightly to the hinge, pyrazolopyrimidines gain an advantage in potency through participation of N4 in an H-bond network involving two catalytic residues and bridging water molecules. Further insight into inhibitor/CDK2 interactions was gained from analysis of additional crystal structures. Significant gains in potency were obtained by optimizing the fit of hydrophobic substituents to the gatekeeper region of the ATP binding site. The most potent inhibitors have good selectivity.

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Organizational Affiliation: 

Schering-Plough Research Institute, Kenilworth, NJ 07033, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division protein kinase 2	A	299	Homo sapiens	Mutation(s): 0  Gene Names: CDK2, CDKN2 EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens) Explore P24941  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
2SC	A	(5-phenyl-7-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-3-yl)methanol C19 H17 N5 O RBLKWWBHDUBPFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2SC	IC50:  600   nM  Binding MOAD
2SC	IC50 :  600   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.1	α = 90
b = 70.22	β = 90
c = 71.84	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-29 
• Released Date: 2008-01-22 
Deposition Author(s): Fischmann, T.O., Hruza, A.W., Madison, V.M., Duca, J.S.

Revision History 

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance