2QD9

P38 Alpha Map Kinase inhibitor based on heterobicyclic scaffolds

• PDB DOI: https://doi.org/10.2210/pdb2QD9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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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 

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

• PubMed: 17664068 
• DOI: https://doi.org/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. X-ray co-crystallography of an oxalamide analog (24) bound to unphosphorylated p38alpha is also disclosed.

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Organizational Affiliation: 

Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.66 kDa 
• Atom Count: 2,850 
• Modelled Residue Count: 330 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	366	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 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 GTEx:  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LGF	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

Binding Affinity Annotations
ID	Source	Binding Affinity
LGF	BindingDB:  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 = 65.65	α = 90
b = 74.36	β = 90
c = 78.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Refinement description