9F1M

First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45

PDB DOI: https://doi.org/10.2210/pdb9F1M/pdb

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

Deposited: 2024-04-19 Released: 2024-09-11
Deposition Author(s): Balourdas, D.I., Edmonds, A.K., Marsh, G.P., Maple, H.J., Spencer, J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.237
R-Value Work: 0.196
R-Value Observed: 0.198

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

First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45

Balourdas, D.I., Edmonds, A.K., Marsh, G.P., Maple, H.J., Spencer, J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 65.29 kDa
Atom Count: 4,481
Modelled Residue Count: 497
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B, C, D	127	Homo sapiens	Mutation(s): 0 Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885 Go to UniProtKB: O60885
PHAROS: O60885 GTEx: ENSG00000141867
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H80 (Subject of Investigation/LOI) Query on A1H80 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	G [auth A], I [auth B], L [auth C], N [auth D]	1-[2-[7-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]heptanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide C₆₂ H₈₅ N₁₁ O₇ S ITTBTKCGUXDYKB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	E [auth A], H [auth B], J [auth C], K [auth C], O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain O [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	F [auth A], M [auth C], P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [auth C] Focus chain P [auth D]