8QOW | pdb_00008qow

LTA4 hydrolase in complex with compound 2(S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.237 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QOW

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Amino Alcohols as Highly Potent, Selective, and Orally Efficacious Inhibitors of Leukotriene A4 Hydrolase.

Thoma, G.Markert, C.Lueoend, R.Miltz, W.Spanka, C.Bollbuck, B.Wolf, R.M.Srinivas, H.Penno, C.A.Kiffe, M.Gajewska, M.Bednarczyk, D.Wieczorek, G.Evans, A.Beerli, C.Rohn, T.A.

(2023) J Med Chem 66: 16410-16425

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01866
  • Primary Citation Related Structures: 
    8QOW, 8QPN, 8QQ4

  • PubMed Abstract: 

    The discovery of chiral amino alcohols derived from our previously disclosed clinical LTA4H inhibitor LYS006 is described. In a biochemical assay, their optical antipodes showed similar potencies, which could be rationalized by the cocrystal structures of these compounds bound to LTA4H. Despite comparable stabilities in liver microsomes, they showed distinct in vivo PK properties. Selective O -phosphorylation of the ( R )-enantiomers in blood led to clearance values above the hepatic blood flow, whereas the ( S )-enantiomers were unaffected and exhibited satisfactory metabolic stabilities in vivo. Introduction of two pyrazole rings led to compound ( S )- 2 with a more balanced distribution of polarity across the molecule, exhibiting high selectivity and excellent potency in vitro and in vivo. Furthermore, compound ( S )- 2 showed favorable profiles in 16-week IND-enabling toxicology studies in dogs and rats. Based on allometric scaling and potency in whole blood, compound ( S )- 2 has the potential for a low oral efficacious dose administered once daily.


  • Organizational Affiliation
    • Global Discovery Chemistry, Biomedical Research, Novartis Pharma AG, 4002 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 70.45 kDa 
  • Atom Count: 5,348 
  • Modeled Residue Count: 607 
  • Deposited Residue Count: 613 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase613Homo 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
WID
(Subject of Investigation/LOI)

Query on WID



Download:Ideal Coordinates CCD File
H [auth A](2~{S})-2-azanyl-3-[3-[4-[3-fluoranyl-5-(1~{H}-pyrazol-5-yl)pyridin-2-yl]oxyphenyl]pyrazol-1-yl]propan-1-ol
C20 H19 F N6 O2
NQHGXSVGARINPB-HNNXBMFYSA-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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.237 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.845α = 90
b = 87.182β = 90
c = 98.858γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-12-06 
  • Deposition Author(s): Srinivas, H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary