8VHM | pdb_00008vhm

Structure of DHODH in Complex with Fragment 2

PDB DOI: https://doi.org/10.2210/pdb8VHM/pdb

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

Deposited: 2024-01-02 Released: 2024-04-03
Deposition Author(s): Shaffer, P.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.228 (Depositor), 0.231 (DCC)
R-Value Work:
0.196 (Depositor), 0.216 (DCC)
R-Value Observed:
0.197 (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

Discovery of Alternative Binding Poses through Fragment-Based Identification of DHODH Inhibitors.

DeRatt, L.G., Pietsch, E.C., Cisar, J.S., Jacoby, E., Kazmi, F., Matico, R., Shaffer, P., Tanner, A., Wang, W., Attar, R., Edwards, J.P., Kuduk, S.D.

(2024) ACS Med Chem Lett 15: 381-387

PubMed: 38505861 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.3c00543
Primary Citation Related Structures:
8VHL, 8VHM

PubMed Abstract:
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial enzyme that affects many aspects essential to cell proliferation and survival. Recently, DHODH has been identified as a potential target for acute myeloid leukemia therapy. Herein, we describe the identification of potent DHODH inhibitors through a scaffold hopping approach emanating from a fragment screen followed by structure-based drug design to further improve the overall profile and reveal an unexpected novel binding mode. Additionally, these compounds had low P-gp efflux ratios, allowing for applications where exposure to the brain would be required.

Organizational Affiliation

Janssen Pharmaceutical Research and Development, 1400 McKean Rd., Spring House, Pennsylvania 19477, United States.

Macromolecule Content

Total Structure Weight: 41.34 kDa
Atom Count: 3,125
Modeled Residue Count: 363
Deposited Residue Count: 369
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	369	Homo sapiens	Mutation(s): 0 Gene Names: DHODH EC: 1.3.5.2
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]
A1AA1 (Subject of Investigation/LOI) Query on A1AA1 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]	N-{4-[(R)-cyclohexyl(hydroxy)methyl]phenyl}acetamide C₁₅ H₂₁ N O₂ JGDCZRXYVXBBMP-OAHLLOKOSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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 E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A]	G [auth A], I [auth A], J [auth A], L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A]	H [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain K [auth A]