7AV2

LTA4 hydrolase in complex with fragment1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery of LYS006, a Potent and Highly Selective Inhibitor of Leukotriene A 4 Hydrolase.

Markert, C.Thoma, G.Srinivas, H.Bollbuck, B.Luond, R.M.Miltz, W.Walchli, R.Wolf, R.Hinrichs, J.Bergsdorf, C.Azzaoui, K.Penno, C.A.Klein, K.Wack, N.Jager, P.Hasler, F.Beerli, C.Loetscher, P.Dawson, J.Wieczorek, G.Numao, S.Littlewood-Evans, A.Rohn, T.A.

(2021) J Med Chem 64: 1889-1903

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01955
  • Primary Citation of Related Structures:  
    7AUZ, 7AV0, 7AV1, 7AV2

  • PubMed Abstract: 

    The cytosolic metalloenzyme leukotriene A 4 hydrolase (LTA4H) is the final and rate-limiting enzyme in the biosynthesis of pro-inflammatory leukotriene B 4 (LTB 4 ). Preclinical studies have validated this enzyme as an attractive drug target in chronic inflammatory diseases. Despite several attempts, no LTA4H inhibitor has reached the market, yet. Herein, we disclose the discovery and preclinical profile of LYS006, a highly potent and selective LTA4H inhibitor. A focused fragment screen identified hits that could be cocrystallized with LTA4H and inspired a fragment merging. Further optimization led to chiral amino acids and ultimately to LYS006, a picomolar LTA4H inhibitor with exquisite whole blood potency and long-lasting pharmacodynamic effects. Due to its high selectivity and its ability to fully suppress LTB 4 generation at low exposures in vivo , LYS006 has the potential for a best-in-class LTA4H inhibitor and is currently investigated in phase II clinical trials in inflammatory acne, hidradenitis suppurativa, ulcerative colitis, and NASH.


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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RZN (Subject of Investigation/LOI)
Query on RZN

Download Ideal Coordinates CCD File 
H [auth A](4-phenoxyphenyl)methanol
C13 H12 O2
FEOMFFKZOZMBKD-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
RZN BindingDB:  7AV2 IC50: 4500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.818α = 90
b = 87.025β = 90
c = 98.888γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-02-17 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-03-03
    Changes: Database references
  • Version 1.3: 2021-03-10
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Data collection, Database references, Refinement description