3LFN

Crystal structure of CDK2 with SAR57, an aminoindazole type inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3LFN/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.268 
• R-Value Work: 0.184 
• R-Value Observed: 0.190 

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 of 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.

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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: 34.35 kDa 
• Atom Count: 2,467 
• Modelled Residue Count: 285 
• 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
A27	B [auth A]	N-[6-(4-hydroxyphenyl)-5-phenyl-1H-indazol-3-yl]butanamide C23 H21 N3 O2 KYYOHACAJWYNOT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A27	Binding MOAD:  3LFN	IC50: 3160 (nM) from 1 assay(s)
	PDBBind:  3LFN	IC50: 3160 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.268 
• R-Value Work: 0.184 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.337	α = 90
b = 72.066	β = 90
c = 71.439	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data processing
TNT	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
BUSTER	refinement

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