1M7Q

Crystal structure of p38 MAP kinase in complex with a dihydroquinazolinone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1M7Q/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-07-22 Released: 2002-12-11 
• Deposition Author(s): Stelmach, J.E., Liu, L., Patel, S.B., Pivnichny, J.V., Scapin, G., Singh, S., Hop, C.E.C.A., Wang, Z., Cameron, P.M., Nichols, E.A., O'Keefe, S.J., O'Neill, E.A., Schmatz, D.M., Schwartz, C.D., Thompson, C.M., Zaller, D.M., Doherty, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 

Starting Model: experimental

Literature

Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase.

Stelmach, J.E., Liu, L., Patel, S.B., Pivnichny, J.V., Scapin, G., Singh, S., Hop, C.E., Wang, Z., Strauss, J.R., Cameron, P.M., Nichols, E.A., O'Keefe, S.J., O'Neill, E.A., Schmatz, D.M., Schwartz, C.D., Thompson, C.M., Zaller, D.M., Doherty, J.B.

(2003) Bioorg Med Chem Lett 13: 277-280

• PubMed: 12482439 
• DOI: https://doi.org/10.1016/s0960-894x(02)00752-7
• Primary Citation of Related Structures:  
  1M7Q


• PubMed Abstract: 
  

  The development of potent, orally bioavailable (in rat) and selective dihydroquinazolinone inhibitors of p38alpha MAP kinase is described. These analogues are hybrids of a pyridinylimidazole p38alpha inhibitor reported by Merck Research Laboratories and VX-745. Optimization of the C-5 phenyl and the C-7 piperidinyl substituents led to the identification of 15i which gave excellent suppression of TNF-alpha production in LPS-stimulated whole blood (IC(50)=10nM) and good oral exposure in rats (F=68%, AUCn PO=0.58 microM h).

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, 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: 42.58 kDa 
• Atom Count: 2,952 
• Modelled Residue Count: 348 
• 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  EC: 2.7.1 (PDB Primary Data), 2.7.11.24 (UniProt)
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQO	C [auth A]	1-(2,6-DICHLOROPHENYL)-5-(2,4-DIFLUOROPHENYL)-7-PIPERAZIN-1-YL-3,4-DIHYDROQUINAZOLIN-2(1H)-ONE C24 H20 Cl2 F2 N4 O YAWZIQKDHQIHOS-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
DQO	BindingDB:  1M7Q	IC50: min: 2.6, max: 67 (nM) from 5 assay(s)
	PDBBind:  1M7Q	IC50: 2.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.516	α = 90
b = 87.163	β = 90
c = 124.939	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
X-GEN	data reduction
CNS	refinement
X-GEN	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-11 
Deposition Author(s): Stelmach, J.E., Liu, L., Patel, S.B., Pivnichny, J.V., Scapin, G., Singh, S., Hop, C.E.C.A., Wang, Z., Cameron, P.M., Nichols, E.A., O'Keefe, S.J., O'Neill, E.A., Schmatz, D.M., Schwartz, C.D., Thompson, C.M., Zaller, D.M., Doherty, J.B.

Revision History  

• Version 1.0: 2002-12-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Structure summary
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description