7OPN

Human Aldehyde Oxidase SNP R1231H in complex with Raloxifene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interrogating the Inhibition Mechanisms of Human Aldehyde Oxidase by X-ray Crystallography and NMR Spectroscopy: The Raloxifene Case.

Mota, C.Diniz, A.Coelho, C.Santos-Silva, T.Esmaeeli, M.Leimkuhler, S.Cabrita, E.J.Marcelo, F.Romao, M.J.

(2021) J Med Chem 64: 13025-13037

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01125
  • Primary Citation of Related Structures:  
    7OPN, 7ORC

  • PubMed Abstract: 

    Human aldehyde oxidase (hAOX1) is mainly present in the liver and has an emerging role in drug metabolism, since it accepts a wide range of molecules as substrates and inhibitors. Herein, we employed an integrative approach by combining NMR, X-ray crystallography, and enzyme inhibition kinetics to understand the inhibition modes of three hAOX1 inhibitors-thioridazine, benzamidine, and raloxifene. These integrative data indicate that thioridazine is a noncompetitive inhibitor, while benzamidine presents a mixed type of inhibition. Additionally, we describe the first crystal structure of hAOX1 in complex with raloxifene. Raloxifene binds tightly at the entrance of the substrate tunnel, stabilizing the flexible entrance gates and elucidating an unusual substrate-dependent mechanism of inhibition with potential impact on drug-drug interactions. This study can be considered as a proof-of-concept for an efficient experimental screening of prospective substrates and inhibitors of hAOX1 relevant in drug discovery.


  • Organizational Affiliation

    Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde oxidase
A, B
1,338Homo sapiensMutation(s): 1 
Gene Names: AOX1AO
EC: 1.2.3.1 (PDB Primary Data), 1.17.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q06278 (Homo sapiens)
Explore Q06278 
Go to UniProtKB:  Q06278
PHAROS:  Q06278
GTEx:  ENSG00000138356 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06278
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A],
R [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
RAL (Subject of Investigation/LOI)
Query on RAL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
V [auth B],
W [auth B]
RALOXIFENE
C28 H27 N O4 S
GZUITABIAKMVPG-UHFFFAOYSA-N
MTE
Query on MTE

Download Ideal Coordinates CCD File 
E [auth A],
P [auth B]
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
PG6
Query on PG6

Download Ideal Coordinates CCD File 
I [auth A]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
N [auth B],
O [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS
Query on MOS

Download Ideal Coordinates CCD File 
F [auth A],
Q [auth B]
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
MLI
Query on MLI

Download Ideal Coordinates CCD File 
H [auth A],
T [auth B]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
U [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RAL BindingDB:  7OPN Ki: min: 0.87, max: 2.3 (nM) from 2 assay(s)
IC50: min: 3, max: 500 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.528α = 90
b = 149.528β = 90
c = 269.488γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BBB-BEP/1185/2014

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description