3LFQ | pdb_00003lfq

Crystal structure of CDK2 with SAR60, an aminoindazole type inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LFQ/pdb

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


• Deposited: 2010-01-18 Released: 2010-03-02 
• Deposition Author(s): Dreyer, M.K., Wendt, K.U., Schimanski-Breves, S., Loenze, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.241 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.195 (DCC) 

Literature

Rational design of potent GSK3beta inhibitors with selectivity for Cdk1 and Cdk2.

Lesuisse, D., Dutruc-Rosset, G., Tiraboschi, G., Dreyer, M.K., Maignan, S., Chevalier, A., Halley, F., Bertrand, P., Burgevin, M.C., Quarteronet, D., Rooney, T.

(2010) Bioorg Med Chem Lett 20: 1985-1989

• PubMed: 20167481 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.114
• Primary Citation Related Structures: 
  3LAU, 3LFN, 3LFQ, 3LFS


• PubMed Abstract: 
  

  From an HTS hit, a series of potent and selective inhibitors of GSK3beta have been designed based on a Cdk2-homology model and with the help of several crystal structures of the compounds within Cdk2.

---

Organizational Affiliation: 
• Medicinal Chemistry, 13 Quai Jules Guesde, 94300 Vitry-sur-Seine, France. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.29 kDa 
• Atom Count: 2,530 
• Modeled Residue Count: 289 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A28	B [auth A]	N-(6,7-difluoro-5-phenyl-1H-indazol-3-yl)butanamide C17 H15 F2 N3 O TZFLUWBMBJLZQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.241 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.195 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.22	α = 90
b = 72.74	β = 90
c = 72.01	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Dreyer, M.K., Wendt, K.U., Schimanski-Breves, S., Loenze, P.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations