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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Related Citations: 

• Biphenyl amide p38 kinase inhibitors 2: Optimisation and SAR
  Angell, R.M., Angell, T.D., Bamborough, P., Brown, D., Brown, M., Buckton, J.B., Cockerill, S.G., Edwards, C.D., Jones, K.L., Longstaff, T., Smee, P.A., Smith, K.J., Somers, D.O., Walker, A.L., Willson, M.
  (2008) Bioorg Med Chem Lett 18: 324

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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  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

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)
	Binding MOAD:  2ZB0	Ki: 240 (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