7T6C

E. coli dihydroorotate dehydrogenase bound to the ubiquinone surrogate DCIP

PDB DOI: https://doi.org/10.2210/pdb7T6C/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2021-12-13 Released: 2022-03-02
Deposition Author(s): Horwitz, S.M., Ambarian, J.A., Davis, K.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.226
R-Value Work: 0.203
R-Value Observed: 0.204

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines.

Horwitz, S.M., Blue, T.C., Ambarian, J.A., Hoshino, S., Seyedsayamdost, M.R., Davis, K.M.

(2022) RSC Chem Biol 3: 420-425

PubMed: 35441142 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/d1cb00255d
Primary Citation of Related Structures:
7T5K, 7T5Y, 7T6C, 7T6H

PubMed Abstract:
Hydroxyalkylquinolines (HAQs) are ubiquitious natural products but their interactions with associated protein targets remain elusive. We report X-ray crystal structures of two HAQs in complex with dihydroorotate dehydrogenase (DHODH). Our results reveal the structural basis of DHODH inhibition by HAQs and open the door to downstream structure-activity relationship studies.

Organizational Affiliation

Department of Chemistry, Emory University Atlanta GA 30322 USA katherine.davis@emory.edu.

Macromolecule Content

Total Structure Weight: 82.78 kDa
Atom Count: 5,340
Modelled Residue Count: 670
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (quinone)	A, B	368	Escherichia coli K-12	Mutation(s): 0 Gene Names: pyrD, b0945, JW0928 EC: 1.3.5.2
UniProt
Find proteins for P0A7E1 (Escherichia coli (strain K12)) Explore P0A7E1 Go to UniProtKB: P0A7E1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A7E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
PE4 Query on PE4 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]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
RLM (Subject of Investigation/LOI) Query on RLM Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	2,6-bis(chloranyl)-4-[(4-hydroxyphenyl)amino]phenol C₁₂ H₉ Cl₂ N O₂ IFTGQCOAUCEONK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
ORO (Subject of Investigation/LOI) Query on ORO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]