4NJ3 | pdb_00004nj3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4NJ3

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2013.11.041
  • Primary Citation 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.


  • Organizational Affiliation
    • Merck Research Laboratories, 320 Bent Street, Cambridge, MA 02141, USA. Electronic address: yongqi.deng@merck.com.

Macromolecule Content 

  • Total Structure Weight: 34.54 kDa 
  • Atom Count: 2,478 
  • Modeled Residue Count: 282 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2299Homo sapiensMutation(s): 1 
Gene Names: CDK2CDKN2
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2KD

Query on 2KD



Download:Ideal Coordinates CCD File
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
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.83α = 90
b = 72.37β = 90
c = 72.42γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary