6Q4J

CDK2 in complex with FragLite34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

    Department of Pathology, St. Olavs Hospital, Trondheim, Norway.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA. Michael.Acker@novartis.com.,State Key Laboratory of Membrane Biology, Beijing, 100084 China.,Northern Institute for Cancer Research, Medical School , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4HH , U.K.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden.,Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France.,Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA.,Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.,Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,3Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084 China.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,4Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Beijing Advanced Innovation Center for Structural Biology, Beijing, 100084 China.,5Present Address: Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. Stephen_Blacklow@hms.harvard.edu.,LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. Stephen_Blacklow@hms.harvard.edu.,Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France.,Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.,Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands. b.j.c.janssen@uu.nl.




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HHB
Query on HHB

Download SDF File 
Download CCD File 
A
2-[3-(pyrimidin-4-ylamino)phenyl]ethanoic acid
C12 H11 N3 O2
BMWRKSIJFRXVQQ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.123α = 90.00
b = 72.348β = 90.00
c = 71.886γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

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
  • Version 1.2: 2019-05-08
    Type: Data collection, Derived calculations