2ZB0

Crystal structure of P38 in complex with biphenyl amide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2ZB0/pdb

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


• Deposited: 2007-10-13 Released: 2008-01-15 
• Deposition Author(s): Somers, D.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.212 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Biphenyl amide p38 kinase inhibitors 1: Discovery and binding mode

Angell, R.M., Bamborough, P., Cleasby, A., Cockerill, S.G., Jones, K.L., Mooney, C.J., Somers, D.O., Walker, A.L.

(2008) Bioorg Med Chem Lett 18: 318-323

• PubMed: 18006306 
• DOI: https://doi.org/10.1016/j.bmcl.2007.10.076
• Primary Citation of Related Structures:  
  2ZAZ, 2ZB0, 2ZB1


• PubMed Abstract: 
  

  The biphenyl amides (BPAs) are a novel series of p38 MAP kinase inhibitors. The discovery of the series through structure-based focused screening is described, and the binding mode of the compounds is explained with reference to X-ray crystal structures.

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Organizational Affiliation: 

GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, 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: 41.83 kDa 
• Atom Count: 3,136 
• Modelled Residue Count: 349 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  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
GK3	B [auth A]	N-(3-cyanophenyl)-2'-methyl-5'-(5-methyl-1,3,4-oxadiazol-2-yl)-4-biphenylcarboxamide C24 H18 N4 O2 PMMLSQFPBFKLHH-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GK3	PDBBind:  2ZB0	Ki: 240 (nM) from 1 assay(s)
	BindingDB:  2ZB0	Ki: 240 (nM) from 1 assay(s)
		IC50: 1500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.212 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.378	α = 90
b = 85.716	β = 90
c = 124.661	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Somers, D.O.

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations