2I0H

The structure of p38alpha in complex with an arylpyridazinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

p38 MAP Kinase Inhibitors Part 6: 2-Arylpyridazin-3-ones as templates for inhibitor design.

Natarajan, S.R.Heller, S.T.Nam, K.Singh, S.B.Scapin, G.Patel, S.Fitzgerald, C.E.Thompson, J.E.O'Keefe, S.J.

(2006) Bioorg.Med.Chem.Lett. 16: 5809-5813

  • DOI: 10.1016/j.bmcl.2006.08.074

  • PubMed Abstract: 
  • p38 inhibitors based on 3,4-dihydropyrido[4,3-d]pyrimidazin-2-one template were synthesized and their SAR explored. Benchmark compounds 30, 35, and 36 were found to be potent against the enzyme. Crystal structure of p38 in complex with 30 indicated a ...

    p38 inhibitors based on 3,4-dihydropyrido[4,3-d]pyrimidazin-2-one template were synthesized and their SAR explored. Benchmark compounds 30, 35, and 36 were found to be potent against the enzyme. Crystal structure of p38 in complex with 30 indicated a key pi-stacking interaction with the pendant tyrosine residue-35 in the glycine-rich loop.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA. ravi_natarajan@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 14
A
366Homo sapiensMutation(s): 1 
Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
222
Query on 222

Download SDF File 
Download CCD File 
A
2-(3-{(2-CHLORO-4-FLUOROPHENYL)[1-(2-CHLOROPHENYL)-6-OXO-1,6-DIHYDROPYRIDAZIN-3-YL]AMINO}PROPYL)-1H-ISOINDOLE-1,3(2H)-DIONE
C27 H19 Cl2 F N4 O3
QGJNGXXVCVFADC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
222IC50: 9 nM (99) BINDINGDB
222IC50: 9 nM BINDINGMOAD
222IC50: 9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.722α = 90.00
b = 88.225β = 90.00
c = 121.456γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MAR345data collection
DENZOdata reduction
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description