6BL3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1074/jbc.RA119.007405
  • Primary Citation of Related Structures:  
    6BL3, 6BL4

  • 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 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 1 and 2) at 2.22-Å resolution. Both compounds are COX-2-selective inhibitors with IC 50 values of 0.76 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 WT enzyme. Inhibition kinetics of compound 2 were similar to those of the indomethacin parent compound against WT COX-2, and the R120A substitution reduced the time dependence 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

    From the A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry, and Pharmacology, Vanderbilt Institute of Chemical Biology, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin G/H synthase 2
A, B, C, D
587Mus musculusMutation(s): 0 
Gene Names: Ptgs2Cox-2Cox2Pghs-bTis10
EC: 1.14.99.1
Membrane Entity: Yes 
UniProt
Find proteins for Q05769 (Mus musculus)
Explore Q05769 
Go to UniProtKB:  Q05769
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05769
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L7M
Query on L7M

Download Ideal Coordinates CCD File 
CA [auth D],
L [auth A],
R [auth B],
W [auth C]
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
HEM
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth D],
K [auth A],
Q [auth B],
V [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BOG
Query on BOG

Download Ideal Coordinates CCD File 
DA [auth D]
M [auth A]
N [auth A]
S [auth B]
X [auth C]
DA [auth D],
M [auth A],
N [auth A],
S [auth B],
X [auth C],
Y [auth C]
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
I [auth A]
J [auth A]
O [auth B]
P [auth B]
AA [auth D],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
T [auth C],
U [auth C],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.474α = 90
b = 121.776β = 123.48
c = 134.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2019-06-12
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary