Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.56 kDa 
• Atom Count: 409 
• Modelled Residue Count: 328 
• Deposited Residue Count: 366 
• Unique protein chains: 1

1IAN

HUMAN P38 MAP KINASE INHIBITOR COMPLEX

• PDB DOI: 10.2210/pdb1IAN/pdb

• Classification: SERINE/THREONINE-PROTEIN KINASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-03-07 Released: 1998-05-06 
• Deposition Author(s): Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.301 
• R-Value Work: 0.234 
• R-Value Observed: 0.234 

Literature

A highly specific inhibitor of human p38 MAP kinase binds in the ATP pocket.

Tong, L., Pav, S., White, D.M., Rogers, S., Crane, K.M., Cywin, C.L., Brown, M.L., Pargellis, C.A.

(1997) Nat Struct Biol 4: 311-316

• PubMed: 9095200 
• DOI: 10.1038/nsb0497-311
• Primary Citation of Related Structures:  
  1IAN


• PubMed Abstract: 
  

The crystal structure of human p38 mitogen-activated protein (MAP) kinase in complex with a potent and highly specific pyridinyl-imidazole inhibitor has been determined at 2.0 A resolution. The structure of the kinase, which is in its unphosphorylated state, is similar to that of the closely-related ERK2. The inhibitor molecule is bound in the ATP pocket. A hydrogen bond is made between the pyridyl nitrogen of the inhibitor and the main chain amido nitrogen of residue 109, analogous to the interaction from the N1 atom of ATP. The crystal structure provides possible explanations for the specificity of this class of inhibitors. Other protein kinase inhibitors may achieve their specificity through a similar mechanism. The structure also reveals a possible second binding site for this inhibitor, with currently unknown function.

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Related Citations: 

• Sb 203580 is a Specific Inhibitor of a Map Kinase Homologue which is Stimulated by Cellular Stresses and Interleukin-1
  Cuenda, A., Rouse, J., Doza, Y.N., Meier, R., Cohen, P., Gallagher, T.F., Young, P.R., Lee, J.C.
  (1995) FEBS Lett 364: 229

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Organizational Affiliation: 

Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P38 MAP KINASE	A	366	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.1 (PDB Primary Data), 2.7.11.24 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D13	B [auth A], C [auth A], D [auth A]	4-[5-(3-IODO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-1H-IMIDAZOL-4-YL]-PYRIDINE C21 H16 I N3 O S RXDZANYWRNIAOR-HHHXNRCGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.301 
• R-Value Work: 0.234 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.1	α = 90
b = 74.3	β = 90
c = 77.9	γ = 90

Software Package:

Software Name	Purpose
MADSYS	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-03-07 
• Released Date: 1998-05-06 
Deposition Author(s): Tong, L.

Revision History  

• Version 1.0: 1998-05-06
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance