Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.1 kDa 
• Atom Count: 3,032 
• Modelled Residue Count: 348 
• Deposited Residue Count: 354 
• Unique protein chains: 1

 3NNU

Crystal structure of P38 alpha in complex with DP1376

• PDB DOI: 10.2210/pdb3NNU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-06-24 Released: 2010-09-15 
• Deposition Author(s): Abendroth, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.227 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region

Ahn, Y.M., Clare, M., Ensinger, C.L., Hood, M.M., Lord, J.W., Lu, W.P., Miller, D.F., Patt, W.C., Smith, B.D., Vogeti, L., Kaufman, M.D., Petillo, P.A., Wise, S.C., Abendroth, J., Chun, L., Clark, R., Feese, M., Kim, H., Stewart, L., Flynn, D.L.

(2010) Bioorg Med Chem Lett 20: 5793-5798

• PubMed: 20800479 
• DOI: 10.1016/j.bmcl.2010.07.134
• Primary Citation of Related Structures:  
  3NNU, 3NNV, 3NNW, 3NNX


• PubMed Abstract: 
  

Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.

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Organizational Affiliation: 

Deciphera Pharmaceuticals LLC, 643 Massachusetts St, Lawrence, KS 66044, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	354	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDB	B [auth A]	2-{3-[(5E)-5-{[(2,3-dichlorophenyl)carbamoyl]imino}-3-thiophen-2-yl-2,5-dihydro-1H-pyrazol-1-yl]phenyl}acetamide C22 H17 Cl2 N5 O2 S YEVPKQHEAVIPSH-NHFJDJAPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EDB	PDBBind:  3NNU	IC50: 48 (nM) from 1 assay(s)
	Binding MOAD:  3NNU	IC50: 48 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.227 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.5	α = 90
b = 86.183	β = 90
c = 126.25	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Abendroth, J.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description