6ENC

LTA4 hydrolase in complex with Compound11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Feasibility and physiological relevance of designing highly potent aminopeptidase-sparing leukotriene A4 hydrolase inhibitors.

Numao, S.Hasler, F.Laguerre, C.Srinivas, H.Wack, N.Jager, P.Schmid, A.Osmont, A.Rothlisberger, P.Houguenade, J.Bergsdorf, C.Dawson, J.Carte, N.Hofmann, A.Markert, C.Hardaker, L.Billich, A.Wolf, R.M.Penno, C.A.Bollbuck, B.Miltz, W.Rohn, T.A.

(2017) Sci Rep 7: 13591-13591

  • DOI: https://doi.org/10.1038/s41598-017-13490-1
  • Primary Citation of Related Structures:  
    6ENB, 6ENC, 6END

  • PubMed Abstract: 

    Leukotriene A4 Hydrolase (LTA4H) is a bifunctional zinc metalloenzyme that comprises both epoxide hydrolase and aminopeptidase activity, exerted by two overlapping catalytic sites. The epoxide hydrolase function of the enzyme catalyzes the biosynthesis of the pro-inflammatory lipid mediator leukotriene (LT) B4. Recent literature suggests that the aminopeptidase function of LTA4H is responsible for degradation of the tripeptide Pro-Gly-Pro (PGP) for which neutrophil chemotactic activity has been postulated. It has been speculated that the design of epoxide hydrolase selective LTA4H inhibitors that spare the aminopeptidase pocket may therefore lead to more efficacious anti-inflammatory drugs. In this study, we conducted a high throughput screen (HTS) for LTA4H inhibitors and attempted to rationally design compounds that would spare the PGP degrading function. While we were able to identify compounds with preference for the epoxide hydrolase function, absolute selectivity was not achievable for highly potent compounds. In order to assess the relevance of designing such aminopeptidase-sparing LTA4H inhibitors, we studied the role of PGP in inducing inflammation in different settings in wild type and LTA4H deficient (LTA4H KO) animals but could not confirm its chemotactic potential.  Attempting to design highly potent epoxide hydrolase selective LTA4H inhibitors, therefore seems to be neither feasible nor relevant.


  • Organizational Affiliation

    Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase613Homo sapiensMutation(s): 0 
EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09960 (Homo sapiens)
Explore P09960 
Go to UniProtKB:  P09960
PHAROS:  P09960
GTEx:  ENSG00000111144 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09960
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGW
Query on BGW

Download Ideal Coordinates CCD File 
H [auth A]1-[[4-(1,3-benzothiazol-2-yloxy)phenyl]methyl]piperidine-4-carboxylic acid
C20 H20 N2 O3 S
BUZBVOKDNAZIIM-UHFFFAOYSA-N
YB
Query on YB

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
BGW BindingDB:  6ENC IC50: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.063α = 90
b = 87.175β = 90
c = 99.154γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-12-13 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Structure summary
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations