7M2O | pdb_00007m2o

Crystal structure of Human Glycolate Oxidase with Inhibitor Compound 15

PDB DOI: https://doi.org/10.2210/pdb7M2O/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-03-17 Released: 2021-07-14
Deposition Author(s): Gumpena, R., Ding, J., Powell, D.A., Lowther, W.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.166 (Depositor), 0.180 (DCC)
R-Value Work:
0.126 (Depositor), 0.135 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Dual Glycolate Oxidase/Lactate Dehydrogenase A Inhibitors for Primary Hyperoxaluria

Ding, J., Gumpena, R., Boily, M.O., Caron, A., Chong, O., Cox, J.H., Dumais, V., Gaudreault, S., Graff, A.H., King, A., Knight, J., Oballa, R., Surendradoss, J., Tang, T., Wu, J., Lowther, W.T., Powell, D.A.

(2021) Acs Medicinal Chemistry Letters 12: 1116-1123

DOI: https://doi.org/10.1021/acsmedchemlett.1c00196

Macromolecule Content

Total Structure Weight: 44.4 kDa
Atom Count: 2,971
Modeled Residue Count: 335
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyacid oxidase 1	A	387	Homo sapiens	Mutation(s): 0 Gene Names: HAO1, GOX1, HAOX1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UJM8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YOJ (Subject of Investigation/LOI) Query on YOJ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid C₃₃ H₂₅ F₂ N₇ O₇ S₂ OLGHHCBVTKMRAO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A]	E [auth A], H [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], G [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A]