6W45

Crystal structure of HAO1 in complex with biaryl acid inhibitor - compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of Novel, Potent Inhibitors of Hydroxy Acid Oxidase 1 (HAO1) Using DNA-Encoded Chemical Library Screening.

Lee, E.C.Y.McRiner, A.J.Georgiadis, K.E.Liu, J.Wang, Z.Ferguson, A.D.Levin, B.von Rechenberg, M.Hupp, C.D.Monteiro, M.I.Keefe, A.D.Olszewski, A.Eyermann, C.J.Centrella, P.Liu, Y.Arora, S.Cuozzo, J.W.Zhang, Y.Clark, M.A.Huguet, C.Kohlmann, A.

(2021) J Med Chem 64: 6730-6744

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02271
  • Primary Citation of Related Structures:  
    6W44, 6W45, 6W4C

  • PubMed Abstract: 

    Inhibition of hydroxy acid oxidase 1 (HAO1) is a strategy to mitigate the accumulation of toxic oxalate that results from reduced activity of alanine-glyoxylate aminotransferase (AGXT) in primary hyperoxaluria 1 (PH1) patients. DNA-Encoded Chemical Library (DECL) screening provided two novel chemical series of potent HAO1 inhibitors, represented by compounds 3 - 6 . Compound 5 was further optimized via various structure-activity relationship (SAR) exploration methods to 29 , a compound with improved potency and absorption, distribution, metabolism, and excretion (ADME)/pharmacokinetic (PK) properties. Since carboxylic acid-containing compounds are often poorly permeable and have potential active glucuronide metabolites, we undertook a brief, initial exploration of acid replacements with the aim of identifying non-acid-containing HAO1 inhibitors. Structure-based drug design initiated with Compound 5 led to the identification of a nonacid inhibitor of HAO1, 31 , which has weaker potency and increased permeability.


  • Organizational Affiliation

    X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxyacid oxidase 1368Homo sapiensMutation(s): 0 
Gene Names: HAO1GOX1HAOX1
EC: 1.1.3.15 (PDB Primary Data), 1.2.3.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJM8 (Homo sapiens)
Explore Q9UJM8 
Go to UniProtKB:  Q9UJM8
PHAROS:  Q9UJM8
GTEx:  ENSG00000101323 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJM8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SLG (Subject of Investigation/LOI)
Query on SLG

Download Ideal Coordinates CCD File 
B [auth A]2-chloranyl-4-[2-[[(6-chloranyl-1~{H}-indol-2-yl)carbonyl-methyl-amino]methyl]-5-fluoranyl-phenyl]benzoic acid
C24 H17 Cl2 F N2 O3
QAUQVYLGWNNTGX-UHFFFAOYSA-N
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SLG BindingDB:  6W45 IC50: min: 110, max: 3.00e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.27α = 90
b = 97.27β = 90
c = 80.458γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description