3ZWS | pdb_00003zws

Structure of Human Dihydroorotate Dehydrogenase with a Bound Inhibitor

PDB DOI: https://doi.org/10.2210/pdb3ZWS/pdb

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

Deposited: 2011-08-02 Released: 2012-06-27
Deposition Author(s): Acklam, P.A., Parsons, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.176 (Depositor), 0.185 (DCC)
R-Value Work:
0.161 (Depositor)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Factors Influencing the Specificity of Inhibitor Binding to the Human and Malaria Parasite Dihydroorotate Dehydrogenases.

Bedingfield, P.T.P., Cowen, D., Acklam, P.A., Cunningham, F., Parsons, M.R., Mcconkey, G.A., Fishwick, C.W.G., Johnson, A.P.

(2012) J Med Chem 55: 5841

PubMed: 22621375 Search on PubMed
DOI: https://doi.org/10.1021/jm300157n
Primary Citation Related Structures:
3ZWS, 3ZWT

PubMed Abstract:
The de novo pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase is an emerging drug target for the treatment of malaria. In this context a key property of Plasmodium falciparum DHODH (PfDHODH) is that it can be selectively inhibited over its human homologue (HsDHODH). However, HsDHODH is also a validated drug target for autoimmune diseases such as arthritis. Here a series of novel inhibitors is described that includes compounds that switch specificity between the two enzymes as a result of small alterations in chemical structure. Structure-activity relationship (SAR), crystallography, docking, and mutagenesis studies are used to examine the binding modes of the compounds within the two enzymes and to reveal structural changes induced by inhibitor binding. Within this series, compounds with therapeutically relevant HsDHODH activity are described and their binding modes characterized using X-ray crystallography, which reveals a novel conformational shift within the inhibitor binding site.

Organizational Affiliation

Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K.

Macromolecule Content

Total Structure Weight: 41.16 kDa
Atom Count: 3,097
Modeled Residue Count: 354
Deposited Residue Count: 367
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL	A	367	Homo sapiens	Mutation(s): 0 EC: 1.3.5.2 (PDB Primary Data), 1.3.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02127 (Homo sapiens) Explore Q02127 Go to UniProtKB: Q02127
PHAROS: Q02127 GTEx: ENSG00000102967
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02127
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN 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]
AVQ Query on AVQ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-[(2,5-DICHLOROBENZYL)SULFANYL]-5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-OL C₁₃ H₁₀ Cl₂ N₄ O S VQASKKWJQGYGRL-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ORO Query on ORO 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]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.176 (Depositor), 0.185 (DCC)
R-Value Work: 0.161 (Depositor)
R-Value Observed: 0.162 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.72	α = 90
b = 90.72	β = 90
c = 123.072	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Acklam, P.A.

Parsons, M.R.

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2012-07-11
Changes: Other
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other