5N3W | pdb_00005n3w

Crystal structure of LTA4H bound to a selective inhibitor against LTB4 generation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The development of novel LTA4H modulators to selectively target LTB4 generation.

Low, C.M.Akthar, S.Patel, D.F.Loser, S.Wong, C.T.Jackson, P.L.Blalock, J.E.Hare, S.A.Lloyd, C.M.Snelgrove, R.J.

(2017) Sci Rep 7: 44449-44449

  • DOI: https://doi.org/10.1038/srep44449
  • Primary Citation Related Structures: 
    5N3W

  • PubMed Abstract: 

    The pro-inflammatory mediator leukotriene B 4 (LTB 4 ) is implicated in the pathologies of an array of diseases and thus represents an attractive therapeutic target. The enzyme leukotriene A 4 hydrolase (LTA 4 H) catalyses the distal step in LTB 4 synthesis and hence inhibitors of this enzyme have been actively pursued. Despite potent LTA 4 H inhibitors entering clinical trials all have failed to show efficacy. We recently identified a secondary anti-inflammatory role for LTA 4 H in degrading the neutrophil chemoattractant Pro-Gly-Pro (PGP) and rationalized that the failure of conventional LTA 4 H inhibitors may be that they inadvertently prevented PGP degradation. We demonstrate that these inhibitors do indeed fail to discriminate between the dual activities of LTA 4 H, and enable PGP accumulation in mice. Accordingly, we have developed novel compounds that potently inhibit LTB 4 generation whilst leaving PGP degradation unperturbed. These novel compounds could represent a safer and superior class of LTA 4 H inhibitors for translation into the clinic.


  • Organizational Affiliation
    • Computational Drug Design Consultant, Dulwich, London SE21 8LS, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 71.02 kDa 
  • Atom Count: 5,310 
  • Modeled Residue Count: 606 
  • Deposited Residue Count: 619 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase619Homo sapiensMutation(s): 0 
Gene Names: LTA4HLTA4
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8KW

Query on 8KW



Download:Ideal Coordinates CCD File
E [auth A]3-[2-(2-hydroxyphenyl)ethyl]-5-methoxy-phenol
C15 H16 O3
IUMFLNFLJUUODE-UHFFFAOYSA-N
YB

Query on YB



Download:Ideal Coordinates CCD File
C [auth A]YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
D [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
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
8KW BindingDB:  5N3W IC50: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.25α = 90
b = 87.05β = 90
c = 99.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom095707/Z/11/Z
Medical Research Council (United Kingdom)United KingdomG1100332/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description