7K2U | pdb_00007k2u

DHODH IN COMPLEX WITH LIGAND 13

PDB DOI: https://doi.org/10.2210/pdb7K2U/pdb

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

Deposited: 2020-09-09 Released: 2020-10-21
Deposition Author(s): Shaffer, P.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.179 (Depositor), 0.190 (DCC)
R-Value Work:
0.165 (Depositor), 0.177 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A carboxylic acid isostere screen of the DHODH inhibitor Brequinar.

DeRatt, L.G., Christine Pietsch, E., Tanner, A., Shaffer, P., Jacoby, E., Wang, W., Kazmi, F., Zhang, X., Attar, R.M., Edwards, J.P., Kuduk, S.D.

(2020) Bioorg Med Chem Lett 30: 127589-127589

PubMed: 33007394 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2020.127589
Primary Citation Related Structures:
7K2U

PubMed Abstract:
Dihydroorotate dehydrogenase (DHODH) enzymatic activity impacts many aspects critical to cell proliferation and survival. Recently, DHODH has been identified as a target for acute myeloid differentiation therapy. In preclinical models of AML, the DHODH inhibitor Brequinar (BRQ) demonstrated potent anti-leukemic activity. Herein we describe a carboxylic acid isostere study of Brequinar which revealed a more potent non-carboxylic acid derivative with improved cellular potency and good pharmacokinetic properties.

Organizational Affiliation

Discovery Chemistry, Janssen Pharmaceutical Research & Development, 1400 McKean Rd, Spring House, PA 19477, USA. Electronic address: lderatt@its.jnj.com.

Macromolecule Content

Total Structure Weight: 41.96 kDa
Atom Count: 3,255
Modeled Residue Count: 366
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 7 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]
VU7 (Subject of Investigation/LOI) Query on VU7 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]	6-fluoro-2-(2'-fluoro[1,1'-biphenyl]-4-yl)-N-methoxy-3-methylquinoline-4-carboxamide C₂₄ H₁₈ F₂ N₂ O₂ XPBXJYBHOVBFDA-UHFFFAOYSA-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]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain G [auth A] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain G [auth A] mmCIF format, chain O [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain G [auth A]	G [auth A], K [auth A], L [auth A], O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A] Interactions & Density Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth A] mmCIF format, chain H [auth A]	H [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth A] Interactions & Density Focus chain H [auth A] Focus chain N [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain J [auth A]