The complex of murine cyclooxygenase-2 with a conjugate of indomefathin and podophyllotoxin, N-{(succinylpodophyllotoxinyl)but-4-yl}-2-{1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3-yl}acetamide

Experimental Data Snapshot

  • Resolution: 2.11 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

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This is version 2.1 of the entry. See complete history


Antitumor Activity of Cytotoxic Cyclooxygenase-2 Inhibitors.

Uddin, M.J.Crews, B.C.Xu, S.Ghebreselasie, K.Daniel, C.K.Kingsley, P.J.Banerjee, S.Marnett, L.J.

(2016) ACS Chem Biol 11: 3052-3060

  • DOI: https://doi.org/10.1021/acschembio.6b00560
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Targeted delivery of chemotherapeutic agents to tumors has been explored as a means to increase the selectivity and potency of cytotoxicity. Most efforts in this area have exploited the molecular recognition of proteins highly expressed on the surface of cancer cells followed by internalization. A related approach that has received less attention is the targeting of intracellular proteins by ligands conjugated to anticancer drugs. An attractive target for this approach is the enzyme cyclooxygenase-2 (COX-2), which is highly expressed in a range of malignant tumors. Herein, we describe the synthesis and evaluation of a series of chemotherapeutic agents targeted to COX-2 by conjugation to indomethacin. Detailed characterization of compound 12, a conjugate of indomethacin with podophyllotoxin, revealed highly potent and selective COX-2 inhibition in vitro and in intact cells. Kinetics and X-ray crystallographic studies demonstrated that compound 12 is a slow, tight-binding inhibitor that likely binds to COX-2's allosteric site with its indomethacin moiety in a conformation similar to that of indomethacin. Compound 12 exhibited cytotoxicity in cell culture similar to that of podophyllotoxin with no evidence of COX-2-dependent selectivity. However, in vivo, compound 12 accumulated selectively in and more effectively inhibited the growth of a COX-2-expressing xenograft compared to a xenograft that did not express COX-2. Compound 12, which we have named chemocoxib A, provides proof-of-concept for the in vivo targeting of chemotherapeutic agents to COX-2 but suggests that COX-2-dependent selectivity may not be evident in cell culture-based assays.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.

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
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
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G, H
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IXP

Download Ideal Coordinates CCD File 
L [auth A],
Q [auth B],
U [auth C],
Z [auth D]
(5S,5aS,8aS,9S)-8-oxo-9-(3,4,5-trimethoxyphenyl)-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4-{[4-({[1-(4-chlorobenzoyl)-5-methoxy-2-methyl-1H-indol-3-yl]acetyl}amino)butyl]amino}-4-oxobutanoate
C49 H50 Cl N3 O13
Query on HEM

Download Ideal Coordinates CCD File 
K [auth A],
P [auth B],
T [auth C],
X [auth D]
C34 H32 Fe N4 O4
Query on BOG

Download Ideal Coordinates CCD File 
M [auth B],
Y [auth D]
octyl beta-D-glucopyranoside
C14 H28 O6
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
N [auth B]
O [auth B]
R [auth C]
I [auth A],
J [auth A],
N [auth B],
O [auth B],
R [auth C],
S [auth C],
V [auth D],
W [auth D]
C8 H15 N O6
Binding Affinity Annotations 
IDSourceBinding Affinity
IXP BindingDB:  4OTJ IC50: min: 90, max: 4000 (nM) from 6 assay(s)
Binding MOAD:  4OTJ IC50: 290 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.11 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.712α = 90
b = 133.943β = 90
c = 122.223γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references
  • Version 1.2: 2017-02-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary