3D7Z

Crystal Structure of P38 Kinase in Complex with a biphenyl amide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3D7Z/pdb

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


• Deposited: 2008-05-22 Released: 2008-07-22 
• Deposition Author(s): Somers, D.O., Patel, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Biphenyl amide p38 kinase inhibitors 3: Improvement of cellular and in vivo activity.

Angell, R., Aston, N.M., Bamborough, P., Buckton, J.B., Cockerill, S., deBoeck, S.J., Edwards, C.D., Holmes, D.S., Jones, K.L., Laine, D.I., Patel, S., Smee, P.A., Smith, K.J., Somers, D.O., Walker, A.L.

(2008) Bioorg Med Chem Lett 18: 4428-4432

• PubMed: 18614366 
• DOI: https://doi.org/10.1016/j.bmcl.2008.06.048
• Primary Citation of Related Structures:  
  3D7Z


• PubMed Abstract: 
  

  The biphenyl amides (BPAs) are a novel series of p38alpha MAP kinase inhibitor. The optimisation of the series to give compounds that are potent in an in vivo disease model is discussed. SAR is presented and rationalised with reference to the crystallographic binding mode.

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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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.9 kDa 
• Atom Count: 3,225 
• 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 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GK5	C [auth A]	N~3~-cyclopropyl-N~4~'-(cyclopropylmethyl)-6-methylbiphenyl-3,4'-dicarboxamide C22 H24 N2 O2 BOPSUAHGQHFKGG-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
GK5	BindingDB:  3D7Z	Ki: min: 9, max: 12.59 (nM) from 4 assay(s)
		IC50: min: 18, max: 1584.89 (nM) from 4 assay(s)
	PDBBind:  3D7Z	Ki: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.63	α = 90
b = 86.103	β = 90
c = 124.811	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Somers, D.O., Patel, S.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-13
  Changes: Structure summary