6BL3

Crystal Complex of Cyclooxygenase-2 with indomethacin-butyldiamine-dansyl conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.217 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Fluorescent indomethacin-dansyl conjugates utilize the membrane-binding domain of cyclooxygenase-2 to block the opening to the active site.

Xu, S.Uddin, M.J.Banerjee, S.Duggan, K.Musee, J.Kiefer, J.R.Ghebreselasie, K.Rouzer, C.A.Marnett, L.J.

(2019) J.Biol.Chem. 294: 8690-8698

  • DOI: 10.1074/jbc.RA119.007405
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many indomethacin amides and esters are cyclooxygenase-2- (COX-2)-selective inhibitors, providing a framework for the design of COX-2-targeted imaging and cancer chemotherapeutic agents. Although previous studies have suggested that the amide or este ...

    Many indomethacin amides and esters are cyclooxygenase-2- (COX-2)-selective inhibitors, providing a framework for the design of COX-2-targeted imaging and cancer chemotherapeutic agents. Although previous studies have suggested that the amide or ester moiety of these inhibitors binds in the lobby region, a spacious alcove within the enzyme's membrane-binding domain, structural details have been lacking. Here, we present observations on the crystal complexes of COX-2 with two indomethacin-dansyl conjugates (compounds 1and 2) at 2.22 Å resolution. Both compounds are COX-2-selective inhibitors with IC 50 values of 0.76 μM and 0.17 μM, respectively. Our results confirmed that the dansyl moiety is localized in and establishes hydrophobic interactions and several hydrogen bonds with the lobby of the membrane binding domain. We noted that in both crystal structures, the linker tethering indomethacin to the dansyl moiety passes through the constriction at the mouth of the COX-2 active site, resulting in displacement and disorder of Arg-120, located at the opening to the active site. Both compounds exhibited higher inhibitory potency against a COX-2 R120A variant than against the wild-type enzyme. Inhibition kinetics of compound 2were similar to those of the indomethacin parent compound against wild-type COX-2, and the R120A substitution reduced the time dependency of COX inhibition. These results provide a structural basis for the further design and optimization of conjugated COX reagents for imaging of malignant or inflammatory tissues containing high COX-2 levels.


    Organizational Affiliation

    Vanderbilt University, United States.,Genentech, United States.,Vanderbilt University School of Medicine, United States.,Cornell University, United States.,Biochemistry, Vanderbilt University, United States.,Dept.of Biochem., Chem. and Pharmacol., Vanderbilt University School of Medicine, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin G/H synthase 2
A, B, C, D
587Mus musculusMutation(s): 0 
Gene Names: Ptgs2 (Cox-2, Cox2, Pghs-b, Tis10)
EC: 1.14.99.1
Find proteins for Q05769 (Mus musculus)
Go to UniProtKB:  Q05769
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
L7M
Query on L7M

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Download CCD File 
A, B, C, D
2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)butyl]acetamide
C35 H37 Cl N4 O5 S
YGEBTZVDTLWCOG-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BOG
Query on BOG

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Download CCD File 
A, B, C, D
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.217 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 215.474α = 90.00
b = 121.776β = 123.48
c = 134.800γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-03-13
    Type: Data collection
  • Version 1.2: 2019-05-15
    Type: Data collection, Database references
  • Version 1.3: 2019-06-12
    Type: Data collection, Database references