6Q4F

CDK2 in complex with FragLite32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

FragLites-Minimal, Halogenated Fragments Displaying Pharmacophore Doublets. An Efficient Approach to Druggability Assessment and Hit Generation.

Wood, D.J.Lopez-Fernandez, J.D.Knight, L.E.Al-Khawaldeh, I.Gai, C.Lin, S.Martin, M.P.Miller, D.C.Cano, C.Endicott, J.A.Hardcastle, I.R.Noble, M.E.M.Waring, M.J.

(2019) J.Med.Chem. 62: 3741-3752

  • DOI: 10.1021/acs.jmedchem.9b00304
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Identifying ligand binding sites on proteins is a critical step in target-based drug discovery. Current approaches to this require resource-intensive screening of large libraries of lead-like or fragment molecules. Here, we describe an efficient and ...

    Identifying ligand binding sites on proteins is a critical step in target-based drug discovery. Current approaches to this require resource-intensive screening of large libraries of lead-like or fragment molecules. Here, we describe an efficient and effective experimental approach to mapping interaction sites using a set of halogenated compounds expressing paired hydrogen-bonding motifs, termed FragLites. The FragLites identify productive drug-like interactions, which are identified sensitively and unambiguously by X-ray crystallography, exploiting the anomalous scattering of the halogen substituent. This mapping of protein interaction surfaces provides an assessment of druggability and can identify efficient start points for the de novo design of hit molecules incorporating the interacting motifs. The approach is illustrated by mapping cyclin-dependent kinase 2, which successfully identifies orthosteric and allosteric sites. The hits were rapidly elaborated to develop efficient lead-like molecules. Hence, the approach provides a new method of identifying ligand sites, assessing tractability and discovering new leads.


    Organizational Affiliation

    Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K.,Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A
306Homo 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
26D
Query on 26D

Download SDF File 
Download CCD File 
A
PYRIDINE-2,6-DIAMINE
C5 H7 N3
VHNQIURBCCNWDN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.187α = 90.00
b = 71.467β = 90.00
c = 72.042γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N009738/1
Cancer Research UKUnited KingdomC2115/A21421

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references