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: 34.54 kDa 
• Atom Count: 2,478 
• Modelled Residue Count: 282 
• Deposited Residue Count: 299 
• Unique protein chains: 1

 4NJ3

Modulating the interaction between CDK2 and Cyclin A with a Quinoline-based inhibitor

• PDB DOI: 10.2210/pdb4NJ3/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-11-08 Released: 2013-11-27 
• Deposition Author(s): Fischmann, T.O., Hruza, A.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.231 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Modulating the interaction between CDK2 and cyclin A with a quinoline-based inhibitor.

Deng, Y., Shipps, G.W., Zhao, L., Siddiqui, M.A., Popovici-Muller, J., Curran, P.J., Duca, J.S., Hruza, A.W., Fischmann, T.O., Madison, V.S., Zhang, R., McNemar, C.W., Mayhood, T.W., Syto, R., Annis, A., Kirschmeier, P., Lees, E.M., Parry, D.A., Windsor, W.T.

(2014) Bioorg Med Chem Lett 24: 199-203

• PubMed: 24332088 
• DOI: 10.1016/j.bmcl.2013.11.041
• Primary Citation of Related Structures:  
  4NJ3


• PubMed Abstract: 
  

A new class of quinoline-based kinase inhibitors has been discovered that both disrupt cyclin dependent 2 (CDK2) interaction with its cyclin A subunit and act as ATP competitive inhibitors. The key strategy for discovering this class of protein-protein disrupter compounds was to screen the monomer CDK2 in an affinity-selection/mass spectrometry-based technique and to perform secondary assays that identified compounds that bound only to the inactive CDK2 monomer and not the active CDK2/cyclin A heterodimer. Through a series of chemical modifications the affinity (Kd) of the original hit improved from 1 to 0.005μM.

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Organizational Affiliation: 

Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 2	A	299	Homo sapiens	Mutation(s): 1  Gene Names: CDK2, CDKN2 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2KD	B [auth A]	6-(3-chlorophenyl)-2-{[(2S)-3-(4-hydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]carbamoyl}quinoline-4-carboxylic acid C27 H21 Cl N2 O6 LTZGVONWBPMCBP-DEOSSOPVSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
2KD	BindingDB:  4NJ3	Ki: 140 (nM) from 1 assay(s)
		Kd: 300 (nM) from 1 assay(s)
		IC50: 1.00e+4 (nM) from 1 assay(s)
	PDBBind:  4NJ3	Kd: 300 (nM) from 1 assay(s)
	Binding MOAD:  4NJ3	Kd: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.231 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.83	α = 90
b = 72.37	β = 90
c = 72.42	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Fischmann, T.O., Hruza, A.W.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2014-01-08
  Changes: Database references