2QD9

P38 Alpha Map Kinase inhibitor based on heterobicyclic scaffolds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and SAR of p38alpha MAP kinase inhibitors based on heterobicyclic scaffolds.

Murali Dhar, T.G.Wrobleski, S.T.Lin, S.Furch, J.A.Nirschl, D.S.Fan, Y.Todderud, G.Pitt, S.Doweyko, A.M.Sack, J.S.Mathur, A.McKinnon, M.Barrish, J.C.Dodd, J.H.Schieven, G.L.Leftheris, K.

(2007) Bioorg Med Chem Lett 17: 5019-5024

  • DOI: 10.1016/j.bmcl.2007.07.029
  • Primary Citation of Related Structures:  
    2QD9

  • PubMed Abstract: 
  • The synthesis and structure-activity relationships (SAR) of p38alpha MAP kinase inhibitors based on heterobicyclic scaffolds are described. This effort led to the identification of compound (21) as a potent inhibitor of p38alpha MAP kinase with good cellular potency toward the inhibition of TNF-alpha production ...

    The synthesis and structure-activity relationships (SAR) of p38alpha MAP kinase inhibitors based on heterobicyclic scaffolds are described. This effort led to the identification of compound (21) as a potent inhibitor of p38alpha MAP kinase with good cellular potency toward the inhibition of TNF-alpha production. X-ray co-crystallography of an oxalamide analog (24) bound to unphosphorylated p38alpha is also disclosed.


    Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. murali.dhar@bms.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A366Homo sapiensMutation(s): 0 
Gene Names: MAPK14CSBPCSBP1CSBP2CSPB1MXI2SAPK2A
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LGF (Subject of Investigation/LOI)
Query on LGF

Download Ideal Coordinates CCD File 
B [auth A]1-[5-[[3-[2,4-bis(fluoranyl)phenyl]-6,8-dihydro-5~{H}-imidazo[1,5-a]pyrazin-7-yl]carbonyl]-6-methoxy-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]ethane-1,2-dione
C27 H24 F2 N6 O5
GRRHHDRNCLEFSY-MRXNPFEDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LGF BindingDB:  2QD9 IC50: 13 (nM) from 1 assay(s)
Binding MOAD:  2QD9 IC50: 13 (nM) from 1 assay(s)
PDBBind:  2QD9 IC50: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.65α = 90
b = 74.36β = 90
c = 78.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2007-06-20 
  • Released Date: 2007-08-21 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-12-12
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary