6SO4

Fragment RZ132 in complex with MAP kinase p38-alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


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Literature

Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes.

Nichols, C.Ng, J.Keshu, A.Kelly, G.Conte, M.R.Marber, M.S.Fraternali, F.De Nicola, G.F.

(2020) J Med Chem 63: 7559-7568

  • DOI: 10.1021/acs.jmedchem.0c00403
  • Primary Citation of Related Structures:  
    6Y80, 6Y81, 6Y7W, 6Y7Y, 6Y7X, 6YCU, 6YCW, 6SO1, 6SOD, 6SOI, 6SO2, 6SO4, 6SPL, 6SOU, 6SOT, 6SOV, 6SP9, 5R86, 5R85, 5R88, 5R87, 5R89, 5R95, 5R94, 5R8V, 5R97, 5R8U, 5R96, 5R8X, 5R99, 5R8W, 5R98, 5R8Z, 5R8Y, 5R8L, 5R8K, 5R8N, 5R8M, 5R8P, 5R91, 5R8O, 5R90, 5R93, 5R8Q, 5R92, 5R8D, 5R8C, 5R8F, 5R8E, 5R8H

  • PubMed Abstract: 
  • Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors ...

    Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it, we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1β-ILR and p38α-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases, the hotspots overlapped with the binding sites of the interacting proteins.


    Organizational Affiliation

    The Randall Centre for Cell & Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A381Mus musculusMutation(s): 0 
Gene Names: Mapk14Crk1Csbp1Csbp2
EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus)
Explore P47811 
Go to UniProtKB:  P47811
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.784α = 90
b = 86.323β = 90
c = 126.699γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
British Heart FoundationUnited KingdomSP/14/2/30922

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references