Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.74 kDa 
• Atom Count: 2825 
• Modelled Residue Count: 335 
• Deposited Residue Count: 360 
• Unique protein chains: 1

4EH6

Human p38 MAP kinase in complex with NP-F5 and RL87

• PDB DOI: 10.2210/pdb4EH6/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-02 Released: 2012-12-05 
• Deposition Author(s): Over, B., Gruetter, C., Waldmann, H., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Natural-product-derived fragments for fragment-based ligand discovery.

Over, B., Wetzel, S., Grutter, C., Nakai, Y., Renner, S., Rauh, D., Waldmann, H.

(2012) Nat Chem 5: 21-28

• PubMed: 23247173 
• DOI: 10.1038/nchem.1506
• Primary Citation of Related Structures:  
  4EH2, 4EH3, 4EH4, 4EH5, 4EH6, 4EH7, 4EH8, 4EH9, 4EHV


• PubMed Abstract: 
  

Fragment-based ligand and drug discovery predominantly employs sp(2)-rich compounds covering well-explored regions of chemical space. Despite the ease with which such fragments can be coupled, this focus on flat compounds is widely cited as contributing to the attrition rate of the drug discovery process. In contrast, biologically validated natural products are rich in stereogenic centres and populate areas of chemical space not occupied by average synthetic molecules. Here, we have analysed more than 180,000 natural product structures to arrive at 2,000 clusters of natural-product-derived fragments with high structural diversity, which resemble natural scaffolds and are rich in sp(3)-configured centres. The structures of the cluster centres differ from previously explored fragment libraries, but for nearly half of the clusters representative members are commercially available. We validate their usefulness for the discovery of novel ligand and inhibitor types by means of protein X-ray crystallography and the identification of novel stabilizers of inactive conformations of p38α MAP kinase and of inhibitors of several phosphatases.

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Organizational Affiliation: 

Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IRG	B [auth A]	N~4~-cyclopropyl-2-phenylquinazoline-4,7-diamine C17 H16 N4 WCANXWUISJCJOB-UHFFFAOYSA-N
0ON	C [auth A]	N-phenylpyridine-3-carboxamide C12 H10 N2 O NYQXIOZBHWFCBU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.12	α = 90
b = 74.65	β = 90
c = 77.31	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-02 
• Released Date: 2012-12-05 
Deposition Author(s): Over, B., Gruetter, C., Waldmann, H., Rauh, D.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references