1S2A | pdb_00001s2a

Crystal structures of prostaglandin D2 11-ketoreductase in complex with the non-steroidal anti-inflammatory drugs flufenamic acid and indomethacin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.198 (Depositor) 
  • R-Value Work: 
    0.172 (Depositor) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structures of prostaglandin D(2) 11-ketoreductase (AKR1C3) in complex with the nonsteroidal anti-inflammatory drugs flufenamic acid and indomethacin.

Lovering, A.L.Ride, J.P.Bunce, C.M.Desmond, J.C.Cummings, S.M.White, S.A.

(2004) Cancer Res 64: 1802-1810

  • DOI: https://doi.org/10.1158/0008-5472.can-03-2847
  • Primary Citation Related Structures: 
    1S1P, 1S1R, 1S2A, 1S2C

  • PubMed Abstract: 

    It is becoming increasingly well established that nonsteroidal anti-inflammatory drugs (NSAID) protect against tumors of the gastrointestinal tract and that they may also protect against a variety of other tumors. These activities have been widely attributed to the inhibition of cylooxygenases (COX) and, in particular, COX-2. However, several observations have indicated that other targets may be involved. Besides targeting COX, certain NSAID also inhibit enzymes belonging to the aldo-keto reductase (AKR) family, including AKR1C3. We have demonstrated previously that overexpression of AKR1C3 acts to suppress cell differentiation and promote proliferation in myeloid cells. However, this enzyme has a broad tissue distribution and therefore represents a novel candidate for the target of the COX-independent antineoplastic actions of NSAID. Here we report on the X-ray crystal structures of AKR1C3 complexed with the NSAID indomethacin (1.8 A resolution) or flufenamic acid (1.7 A resolution). One molecule of indomethacin is bound in the active site, whereas flufenamic acid binds to both the active site and the beta-hairpin loop, at the opposite end of the central beta-barrel. Two other crystal structures (1.20 and 2.1 A resolution) show acetate bound in the active site occupying the proposed oxyanion hole. The data underline AKR1C3 as a COX-independent target for NSAID and will provide a structural basis for the future development of new cancer therapies with reduced COX-dependent side effects.


  • Organizational Affiliation
    • The School of Biosciences, The University of Birmingham, Birmingham, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 39.15 kDa 
  • Atom Count: 2,963 
  • Modeled Residue Count: 315 
  • Deposited Residue Count: 331 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member C3331Homo sapiensMutation(s): 0 
EC: 1.1.1.213 (PDB Primary Data), 1.3.1.20 (PDB Primary Data), 1.1.1.62 (PDB Primary Data), 1.1.1.64 (UniProt), 1.1.1.53 (UniProt), 1.1.1.357 (UniProt), 1.1.1.188 (UniProt), 1.1.1.239 (UniProt), 1.1.1 (UniProt), 1.1.1.210 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42330 (Homo sapiens)
Explore P42330 
Go to UniProtKB:  P42330
PHAROS:  P42330
GTEx:  ENSG00000196139 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42330
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP



Download:Ideal Coordinates CCD File
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
IMN

Query on IMN



Download:Ideal Coordinates CCD File
C [auth A]INDOMETHACIN
C19 H16 Cl N O4
CGIGDMFJXJATDK-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
E [auth A]UNKNOWN ATOM OR ION
X
Binding Affinity Annotations 
IDSourceBinding Affinity
IMN BindingDB:  1S2A Ki: min: 270, max: 1.00e+5 (nM) from 5 assay(s)
IC50: min: 100, max: 1.30e+5 (nM) from 14 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.198 (Depositor) 
  • R-Value Work:  0.172 (Depositor) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.808α = 90
b = 63.074β = 90
c = 96.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description