5R8F

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z2377835233 in complex with INTERLEUKIN-1 BETA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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:  
    5R85, 5R86, 5R87, 5R88, 5R89, 5R8A, 5R8B, 5R8C, 5R8D, 5R8E, 5R8F, 5R8G, 5R8H, 5R8I, 5R8J, 5R8K, 5R8L, 5R8M, 5R8N, 5R8O, 5R8P, 5R8Q, 5R8U, 5R8V, 5R8W, 5R8X, 5R8Y, 5R8Z, 5R90, 5R91, 5R92, 5R93, 5R94, 5R95, 5R96, 5R97, 5R98, 5R99, 5R9A, 5R9B, 5R9C, 5R9D, 5R9E, 5R9F, 5R9G, 5R9H, 5R9I, 5R9J, 5R9K, 5R9L

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-1 betaA153Homo sapiensMutation(s): 0 
Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01584
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K3Y (Subject of Investigation/LOI)
Query on K3Y
Download Ideal Coordinates CCD File 
D [auth A]1-methyl-3-[(3R)-piperidin-3-yl]-1H-pyrazole-4-carboxamide
C10 H16 N4 O
PVGLDQISVNLVSL-SSDOTTSWSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.73α = 90
b = 54.73β = 90
c = 75.25γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-08-05
    Changes: Database references