1P2A

The structure of cyclin dependent kinase 2 (CKD2) with a trisubstituted naphthostyril inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1P2A/pdb

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


• Deposited: 2003-04-15 Released: 2003-07-15 
• Deposition Author(s): Liu, J.-J., Dermatakis, A., Lukacs, C.M., Konzelmann, F., Chen, Y., Kammlott, U., Depinto, W., Yang, H., Yin, X., Chen, Y., Schutt, A., Simcox, M.E., Luk, K.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.280 
• R-Value Work: 0.206 

Literature

3,5,6-Trisubstituted Naphthostyrils as CDK2 Inhibitors

Liu, J.-J., Dermatakis, A., Lukacs, C.M., Konzelmann, F., Chen, Y., Kammlott, U., Depinto, W., Yang, H., Yin, X., Chen, Y., Schutt, A., Simcox, M.E., Luk, K.-C.

(2003) Bioorg Med Chem 13: 2465-2468

• PubMed: 12852944 
• DOI: https://doi.org/10.1016/s0960-894x(03)00488-8
• Primary Citation of Related Structures:  
  1P2A


• PubMed Abstract: 
  

  A novel class of 3,5,6-trisubstituted naphthostyril analogues was designed and synthesized to study the structure-activity relationship for inhibition of cyclin-dependent kinase 2 (CDK2). These compounds, particularly molecules with side-chain modifications providing additional hydrogen bonding capability, were demonstrated to be potent CDK2 inhibitors with cellular activities consistent with CDK2 inhibition. These molecules inhibited tumor cell proliferation and G1-S and G2-M cell-cycle progression in vitro. The X-ray crystal structure of a 2-aminoethyleneamine derivative bound to CDK2, refined to 2.5A resolution, is presented.

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Organizational Affiliation: 

Department of Discovery Chemistry, Hoffmann-La Roche Inc., 340 Kingsland Street, Nutley, NJ 07110, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.29 kDa 
• Atom Count: 2,277 
• Modelled Residue Count: 271 
• 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: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
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
5BN	B [auth A]	5-[(2-AMINOETHYL)AMINO]-6-FLUORO-3-(1H-PYRROL-2-YL)BENZO[CD]INDOL-2(1H)-ONE C17 H15 F N4 O CQCXWWWNUFQYJS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5BN	BindingDB:  1P2A	IC50: 12 (nM) from 1 assay(s)
	PDBBind:  1P2A	IC50: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.280 
• R-Value Work: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.645	α = 90
b = 71.406	β = 90
c = 71.342	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-15 
Deposition Author(s): Liu, J.-J., Dermatakis, A., Lukacs, C.M., Konzelmann, F., Chen, Y., Kammlott, U., Depinto, W., Yang, H., Yin, X., Chen, Y., Schutt, A., Simcox, M.E., Luk, K.-C.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations