9ZLG | pdb_00009zlg

Crystal structure of DCAF1 in complex with SDIPTAC C9

PDB DOI: https://doi.org/10.2210/pdb9ZLG/pdb

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

Deposited: 2025-12-08 Released: 2026-05-20
Deposition Author(s): Mabanglo, M.F., Srivastava, S., Hoffer, L., Ramnauth, J., Vedadi, M.
Funding Organization(s): Ontario Institute for Cancer Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.289 (Depositor), 0.289 (DCC)
R-Value Work:
0.243 (Depositor), 0.243 (DCC)
R-Value Observed:
0.243 (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

Self-dimerization Induced Proximity Targeting Chimeras (SDIPTAC) lead to DCAF1 loss of function and inhibition of HIV replication

Mabanglo, M.F., Vedadi, M.

To be published.

Macromolecule Content

Total Structure Weight: 288.91 kDa
Atom Count: 19,374
Modeled Residue Count: 2,359
Deposited Residue Count: 2,512
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A, B, C, D, E A, B, C, D, E, F, G, H	314	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y4B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C26 (Subject of Investigation/LOI) Query on A1C26 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain M [auth F] MOL2 format, chain K [auth D] MOL2 format, chain M [auth F] mmCIF format, chain K [auth D] mmCIF format, chain M [auth F]	K [auth D], M [auth F]	(4P,4'P)-5,5'-[(1E,36E)-3,35-dioxo-7,10,13,16,19,22,25,28,31-nonaoxa-4,34-diazaheptatriaconta-1,36-diene-1,37-diyl]bis{N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide} C₆₆ H₇₄ Cl₄ F₄ N₈ O₁₅ RFKBBURQJLHJKG-VLMGOEMLSA-N		Interactions Focus chain K [auth D] Focus chain M [auth F] Interactions & Density Focus chain K [auth D] Focus chain M [auth F]
A1C24 (Subject of Investigation/LOI) Query on A1C24 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth C] SDF format, chain L [auth E] SDF format, chain N [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth E] MOL2 format, chain N [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth E] mmCIF format, chain N [auth G]	I [auth A], J [auth C], L [auth E], N [auth G]	(4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-1H-pyrrole-3-carboxamide C₂₀ H₁₅ Cl₂ F₂ N₃ O₂ GMPBLLVISWPXHF-SFHVURJKSA-N		Interactions Focus chain I [auth A] Focus chain J [auth C] Focus chain L [auth E] Focus chain N [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth C] Focus chain L [auth E] Focus chain N [auth G]