9OCM | pdb_00009ocm

Crystal structure of dihydroorotate dehydrogenase from Leishmania brasiliensis in complex with (E)-5-(3-(4-nitrophenyl)allylidene)pyrimidine-2,4,6(1H,3H,5H)-trione

PDB DOI: https://doi.org/10.2210/pdb9OCM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leishmania braziliensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-24 Released: 2026-05-06
Deposition Author(s): Vaidergorn, M.M., Nonato, M.C., Froes, T.Q., Augusto, B.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of dihydroorotate dehydrogenase from Leishmania brasiliensis in complex with (E)-5-(3-(4-nitrophenyl)allylidene)pyrimidine-2,4,6(1H,3H,5H)-trione

Vaidergorn, M.M., Nonato, M.C., Froes, T.Q., Augusto, B.S.

To be published.

Macromolecule Content

Total Structure Weight: 76.75 kDa
Atom Count: 5,314
Modeled Residue Count: 627
Deposited Residue Count: 694
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, B	347	Leishmania braziliensis	Mutation(s): 0 Gene Names: DHODH, LBRM_16_0550 EC: 1.3.3.1 (PDB Primary Data), 1.3.98.1 (UniProt)
UniProt
Find proteins for E9AI53 (Leishmania braziliensis) Explore E9AI53 Go to UniProtKB: E9AI53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E9AI53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
A1CAU (Subject of Investigation/LOI) Query on A1CAU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	(E)-5-(3-(4-nitrophenyl)allylidene)pyrimidine-2,4,6(1H,3H,5H)-trione C₁₃ H₉ N₃ O₅ MLXVJXPSNYDYIR-UPHRSURJSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]