3IPH

Crystal structure of p38 in complex with a biphenylamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3IPH/pdb

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


• Deposited: 2009-08-17 Released: 2009-11-24 
• Deposition Author(s): Somers, D.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

p38alpha mitogen-activated protein kinase inhibitors: optimization of a series of biphenylamides to give a molecule suitable for clinical progression.

Aston, N.M., Bamborough, P., Buckton, J.B., Edwards, C.D., Holmes, D.S., Jones, K.L., Patel, V.K., Smee, P.A., Somers, D.O., Vitulli, G., Walker, A.L.

(2009) J Med Chem 52: 6257-6269

• PubMed: 19772287 
• DOI: https://doi.org/10.1021/jm9004779
• Primary Citation of Related Structures:  
  3IPH


• PubMed Abstract: 
  

  p38alpha MAP kinase is a key anti-inflammatory target for rheumatoid arthritis, influencing biosynthesis of pro-inflammatory cytokines TNFalpha and IL-1beta at a translational and transcriptional level. In this paper, we describe how we have optimized a series of novel p38alpha/beta inhibitors using crystal structures of our inhibitors bound to p38alpha, classical medicinal chemistry, and modeling of virtual libraries to derive a molecule suitable for progression into clinical development.

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Organizational Affiliation: 

GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Rd, 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: 42.37 kDa 
• Atom Count: 3,216 
• Modelled Residue Count: 347 
• 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
G11	B [auth A]	6-[5-(cyclopropylcarbamoyl)-2-methylphenyl]-N-(cyclopropylmethyl)pyridine-3-carboxamide C21 H23 N3 O2 WIXHEGLMUQGJCC-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [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
G11	BindingDB:  3IPH	Ki: min: 9, max: 25.12 (nM) from 2 assay(s)
		IC50: min: 316, max: 316.23 (nM) from 2 assay(s)
	PDBBind:  3IPH	Ki: 25.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.753	α = 90
b = 85.688	β = 90
c = 125.206	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: 2009-11-24 
Deposition Author(s): Somers, D.O.

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary