4AA5

P38ALPHA MAP KINASE BOUND TO CMPD 33

• PDB DOI:  https://doi.org/10.2210/pdb4AA5/pdb

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


• Deposited: 2011-11-30 Released: 2012-05-16 
• Deposition Author(s): Gerhardt, S., Hargreaves, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

The Discovery of N-Cyclopropyl-4-Methyl-3-[6--(4-Methylpiperazin-1-Yl-4-Oxoquinazolin-3(4H)-Yl]Benzamide (Azd6703), a Clinical P38Alpha Map Kinase Inhibitor for the Treatment of Inflammatory Diseases

Brown, D.S., Cumming, J.G., Bethel, P., Finlayson, J., Gerhardt, S., Nash, I., Pauptit, R., Pike, K.G., Reid, A., Snelson, W., Swallow, S., Thompson, C.

(2012) Bioorg Med Chem Lett 22: 3879

• PubMed: 22608965 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.116
• Primary Citation of Related Structures:  
  4A9Y, 4AA0, 4AA4, 4AA5, 4AAC


• PubMed Abstract: 
  

  A novel, potent and selective quinazolinone series of inhibitors of p38α MAP kinase has been identified. Modifications designed to address the issues of poor aqueous solubility and high plasma protein binding as well as embedded aniline functionalities resulted in the identification of a clinical candidate N-cyclopropyl-4-methyl-3-[6-(4-methylpiperazin-1-yl)-4-oxoquinazolin-3(4H)-yl]benzamide (AZD6703). Optimisation was guided by understanding of the binding modes from X-ray crystallographic studies which showed a switch from DFG 'out' to DFG 'in' as the inhibitor size was reduced to improve overall properties.

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Organizational Affiliation: 

AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.49 kDa 
• Atom Count: 2,803 
• Modelled Residue Count: 341 
• Deposited Residue Count: 365 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOGEN-ACTIVATED PROTEIN KINASE 14	A	365	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24 (PDB Primary Data), 2.7.1.37 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NQB	B [auth A]	N-CYCLOPROPYL-4-METHYL-3-[6-(4-METHYLPIPERAZIN-1-YL)-4-OXIDANYLIDENE-QUINAZOLIN-3-YL]BENZAMIDE C24 H27 N5 O2 ZMAZXHICVRYLQN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
NQB	BindingDB:  4AA5	IC50: min: 15.85, max: 50 (nM) from 7 assay(s)
	Binding MOAD:  4AA5	IC50: 16 (nM) from 1 assay(s)
	PDBBind:  4AA5	IC50: 16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.260 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.48	α = 90
b = 74.654	β = 90
c = 76.399	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Gerhardt, S., Hargreaves, D.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Other
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-02-06
  Changes: Data collection, Experimental preparation