5M0M

Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators.

Keune, W.J.Potjewyd, F.Heidebrecht, T.Salgado-Polo, F.Macdonald, S.J.Chelvarajan, L.Abdel Latif, A.Soman, S.Morris, A.J.Watson, A.J.Jamieson, C.Perrakis, A.

(2017) J. Med. Chem. 60: 2006-2017

  • DOI: 10.1021/acs.jmedchem.6b01743
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Autotaxin produces the bioactive lipid lysophosphatidic acid (LPA) and is a drug target of considerable interest for numerous pathologies. We report the expedient, structure-guided evolution of weak physiological allosteric inhibitors (bile salts) in ...

    Autotaxin produces the bioactive lipid lysophosphatidic acid (LPA) and is a drug target of considerable interest for numerous pathologies. We report the expedient, structure-guided evolution of weak physiological allosteric inhibitors (bile salts) into potent competitive Autotaxin inhibitors that do not interact with the catalytic site. Functional data confirms that our lead compound attenuates LPA mediated signaling in cells and reduces LPA synthesis in vivo, providing a promising natural product derived scaffold for drug discovery.


    Organizational Affiliation

    Division of Biochemistry, The Netherlands Cancer Institute , Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
A
827Rattus norvegicusMutation(s): 4 
Gene Names: Enpp2 (Atx, Npps2)
EC: 3.1.4.39
Find proteins for Q64610 (Rattus norvegicus)
Go to UniProtKB:  Q64610
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
IOD
Query on IOD

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
7CF
Query on 7CF

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A
[3,5-bis(chloranyl)phenyl]methyl (3~{R})-3-[[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]pyrrolidine-1-carboxylate
C36 H52 Cl2 N2 O5
ZEXNABOXYLWWLJ-WGEHOESMSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NKP
Query on NKP

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A
(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate
18:1 LPA, oleoyl lysophosphatidic acid
C21 H41 O7 P
WRGQSWVCFNIUNZ-SQUSKLHYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.995α = 90.00
b = 89.173β = 103.12
c = 77.289γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release