5MPJ

1-(2-chloro-[1,1'-biphenyl]-4-yl)-N-methylethanamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A fragment-based approach leading to the discovery of a novel binding site and the selective CK2 inhibitor CAM4066.

De Fusco, C.Brear, P.Iegre, J.Georgiou, K.H.Sore, H.F.Hyvonen, M.Spring, D.R.

(2017) Bioorg Med Chem 25: 3471-3482

  • DOI: https://doi.org/10.1016/j.bmc.2017.04.037
  • Primary Citation of Related Structures:  
    5CT0, 5CTP, 5CU0, 5CU2, 5CX9, 5MMF, 5MMR, 5MO5, 5MO6, 5MO7, 5MO8, 5MOD, 5MOE, 5MOH, 5MOT, 5MOV, 5MOW, 5MP8, 5MPJ

  • PubMed Abstract: 

    Recently we reported the discovery of a potent and selective CK2α inhibitor CAM4066. This compound inhibits CK2 activity by exploiting a pocket located outside the ATP binding site (αD pocket). Here we describe in detail the journey that led to the discovery of CAM4066 using the challenging fragment linking strategy. Specifically, we aimed to develop inhibitors by linking a high-affinity fragment anchored in the αD site to a weakly binding warhead fragment occupying the ATP site. Moreover, we describe the remarkable impact that molecular modelling had on the development of this novel chemical tool. The work described herein shows potential for the development of a novel class of CK2 inhibitors.


  • Organizational Affiliation

    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
352Homo sapiensMutation(s): 1 
Gene Names: CSNK2A1CK2A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
D [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
J2P
Query on J2P

Download Ideal Coordinates CCD File 
E [auth A](3-chloranyl-4-phenyl-phenyl)methyl-ethyl-azanium
C15 H17 Cl N
CUAIXKURSOOKBM-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.76α = 90
b = 68.46β = 90
c = 334.74γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom090340/Z/09/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Advisory, Author supporting evidence
  • Version 2.0: 2020-10-07
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description