7OPN

Human Aldehyde Oxidase SNP R1231H in complex with Raloxifene

PDB DOI: https://doi.org/10.2210/pdb7OPN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2021-06-01 Released: 2021-09-01
Deposition Author(s): Mota, C., Coelho, C., Santos Silva, T., Romao, M.J.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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

PubMed: 34415167 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 302.26 kDa
Atom Count: 20,650
Modelled Residue Count: 2,590
Deposited Residue Count: 2,676
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde oxidase	A, B	1,338	Homo sapiens	Mutation(s): 1 Gene Names: AOX1, AO 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06278
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain R [auth B]	G [auth A], R [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain R [auth B]
RAL (Subject of Investigation/LOI) Query on RAL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	L [auth A], M [auth A], V [auth B], W [auth B]	RALOXIFENE C₂₈ H₂₇ N O₄ S GZUITABIAKMVPG-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain V [auth B] Focus chain W [auth B]
MTE Query on MTE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B]	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		Interactions Focus chain E [auth A] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain P [auth B]
PG6 Query on PG6 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	C [auth A], D [auth A], N [auth B], O [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain N [auth B] Focus chain O [auth B]
MOS Query on MOS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B]	F [auth A], Q [auth B]	DIOXOTHIOMOLYBDENUM(VI) ION H Mo O₂ S BDSRWPHSAKXXRG-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth B] mmCIF format, chain H [auth A]	H [auth A], T [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain T [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B]	J [auth A], K [auth A], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]