8OOD | pdb_00008ood

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15

PDB DOI: https://doi.org/10.2210/pdb8OOD/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2023-04-05 Released: 2023-05-24
Deposition Author(s): Schroeder, M., Renatus, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings

Schroder, M., Renatus, M., Thoma, C.R.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2023.04.09.536153

Macromolecule Content

Total Structure Weight: 43.87 kDa
Atom Count: 3,022
Modeled Residue Count: 300
Deposited Residue Count: 367
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A	367	Homo sapiens	Mutation(s): 1 Gene Names: DCAF1, KIAA0800, RIP, VPRBP EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4B6 (Homo sapiens) Explore Q9Y4B6 Go to UniProtKB: Q9Y4B6
PHAROS: Q9Y4B6 GTEx: ENSG00000145041
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y4B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VY3 (Subject of Investigation/LOI) Query on VY3 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide C₄₂ H₆₂ Cl N₇ O₈ DKUYAWVMZOOWFE-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]