6W45 | pdb_00006w45

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 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.147 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6W45

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 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.

Macromolecule Content 

  • Total Structure Weight: 41.66 kDa 
  • Atom Count: 2,827 
  • Modeled Residue Count: 325 
  • Deposited Residue Count: 368 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.186 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.147 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.149 (Depositor) 
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