4NJ3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2013.11.041

  • 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-prote ...

    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.


    Organizational Affiliation

    Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA. Electronic address: yongqi.deng@merck.com.,Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.,Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA.,Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: william.windsor@merck.com.,Merck Research Laboratories, 901 California Avenue, Palo Alto, CA 94304, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
299Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2KD
Query on 2KD

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.848 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.830α = 90.00
b = 72.370β = 90.00
c = 72.420γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTERphasing
BUSTERrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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