1IAN | pdb_00001ian

HUMAN P38 MAP KINASE INHIBITOR COMPLEX


Experimental Data Snapshot

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

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/nsb0497-311
  • Primary Citation 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.


  • Organizational Affiliation
    • Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
P38 MAP KINASE366Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D13

Query on D13



Download:Ideal Coordinates CCD File
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 (Depositor) 
  • R-Value Work:  0.234 (Depositor) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.1α = 90
b = 74.3β = 90
c = 77.9γ = 90
Software Package:
Software NamePurpose
MADSYSphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description