3FC1

Crystal structure of p38 kinase bound to pyrimido-pyridazinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase.

Pearlman, D.A.

(2005) J Med Chem 48: 7796-7807

  • DOI: 10.1021/jm050306m
  • Primary Citation of Related Structures:  
    3FC1

  • PubMed Abstract: 
  • The recently described molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method for calculating free energies is applied to a congeneric series of 16 ligands to p38 MAP kinase whose binding constants span approximately 2 orders of magnitud ...

    The recently described molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method for calculating free energies is applied to a congeneric series of 16 ligands to p38 MAP kinase whose binding constants span approximately 2 orders of magnitude. These compounds have previously been used to test and compare other free energy calculation methods, including thermodynamic integration (TI), OWFEG, ChemScore, PLPScore, and Dock Energy Score. We find that the MM-PBSA performs relatively poorly for this set of ligands, yielding results much inferior to those from TI or OWFEG, inferior to Dock Energy Score, and not appreciably better than ChemScore or PLPScore but at an appreciably larger computational cost than any of these other methods. This suggests that one should be selective in applying the MM-PBSA method and that for systems that are amenable to other free energy approaches, these other approaches may be preferred. We also examine the single simulation approximation for MM-PBSA, whereby the required ligand and protein trajectories are extracted from a single MD simulation rather than two separate MD runs. This assumption, sometimes used to speed the MM-PBSA calculation, is found to yield significantly inferior results with only a moderate net percentage reduction in total simulation time.


    Related Citations: 
    • Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system.
      Pearlman, D.A., Charifson, P.S.
      (2001) J Med Chem 44: 3417

    Organizational Affiliation

    150 Jason Street, Arlington, Massachusetts 02476, USA. Science@arlingtonmass.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14X366Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
52P
Query on 52P

Download CCD File 
X
5-(2,6-dichlorophenyl)-2-[(2,4-difluorophenyl)sulfanyl]-6H-pyrimido[1,6-b]pyridazin-6-one
C19 H9 Cl2 F2 N3 O S
VEPKQEUBKLEPRA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
52PIC50:  10   nM  BindingDB
52PIC50:  9   nM  BindingDB
52PIC50:  0.800000011920929   nM  BindingDB
52PIC50:  150   nM  BindingDB
52PIC50:  51   nM  BindingDB
52PIC50:  45   nM  BindingDB
52PIC50:  180   nM  BindingDB
52PIC50:  700   nM  BindingDB
52PIC50:  29   nM  BindingDB
52PIC50 :  10   nM  PDBBind
52PKd:  10000   nM  BindingDB
52PKd:  3.200000047683716   nM  BindingDB
52PIC50:  22   nM  BindingDB
52PIC50:  34   nM  BindingDB
52PIC50:  5300   nM  BindingDB
52PKd:  2.799999952316284   nM  BindingDB
52PIC50:  120   nM  BindingDB
52PIC50:  70   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.697α = 90
b = 85.958β = 90
c = 123.271γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
X-PLORmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance