5U6X | pdb_00005u6x

COX-1:P6 COMPLEX STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb5U6X/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ovis aries
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-12-09 Released: 2017-08-09 
• Deposition Author(s): Cingolani, G., Panella, A., Perrone, M.G., Vitale, P., Smith, W.L., Scilimati, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free: 
  0.234 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Structural basis for selective inhibition of Cyclooxygenase-1 (COX-1) by diarylisoxazoles mofezolac and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole (P6).

Cingolani, G., Panella, A., Perrone, M.G., Vitale, P., Di Mauro, G., Fortuna, C.G., Armen, R.S., Ferorelli, S., Smith, W.L., Scilimati, A.

(2017) Eur J Med Chem 138: 661-668

• PubMed: 28710965 
• DOI: https://doi.org/10.1016/j.ejmech.2017.06.045
• Primary Citation Related Structures: 
  5U6X, 5WBE


• PubMed Abstract: 
  

  The diarylisoxazole molecular scaffold is found in several NSAIDs, especially those with high selectivity for COX-1. Here, we have determined the structural basis for COX-1 binding to two diarylisoxazoles: mofezolac, which is polar and ionizable, and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole (P6) that has very low polarity. X-ray analysis of the crystal structures of COX-1 bound to mofezolac and 3-(5-chlorofuran-2-yl)-5-methyl-4-phenylisoxazole allowed the identification of specific binding determinants within the enzyme active site, relevant to generate structure/activity relationships for diarylisoxazole NSAIDs.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Institute of Biomembranes and Bioenergetics, National Research Council, Via Amendola 165/A, 70125 Bari, Italy.
Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy.
Department of Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, Philadelphia, PA 19107, USA.
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125 Bari, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 144.03 kDa 
• Atom Count: 9,344 
• Modeled Residue Count: 1,106 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 1	A, B	600	Ovis aries	Mutation(s): 0  Gene Names: PTGS1, COX1 EC: 1.14.99.1
UniProt
Find proteins for P05979 (Ovis aries) Explore P05979  Go to UniProtKB:  P05979
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E, F, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G27747YT GlyCosmos: G27747YT GlyGen: G27747YT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	I [auth A], L [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BOG	K [auth A], N [auth B], O [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
P6A	J [auth A], M [auth B]	3-(5-chlorofuran-2-yl)-5-methyl-4-phenyl-1,2-oxazole C14 H10 Cl N O2 IPAVFMUBTIUYBW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P6A	BindingDB:  5U6X	IC50: min: 500, max: 3.90e+4 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.93 Å
• R-Value Free:  0.234 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.463	α = 90
b = 181.463	β = 90
c = 103.5	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Cingolani, G., Panella, A., Perrone, M.G., Vitale, P., Smith, W.L., Scilimati, A.

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary