8UGU | pdb_00008ugu

Crystal structure of the second bromodomain of human BRD2 in complex with 4IND

PDB DOI: https://doi.org/10.2210/pdb8UGU/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-06 Released: 2025-04-02
Deposition Author(s): Nithianantham, S., Fischer, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.195 (Depositor), 0.198 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (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

Development of synthetic molecules for bromodomain-selective recruitment of transcriptional regulators to targeted genomic loci

Chowdhury, N., Nithianantham, S., Lang, W., Young, S., Philips, S., Das, S., Shelat, A., Fischer, M., Ansari, A., Jaisankar, P.

To be published.

Macromolecule Content

Total Structure Weight: 56.24 kDa
Atom Count: 4,034
Modeled Residue Count: 432
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C, D	115	Homo sapiens	Mutation(s): 0 Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440 Go to UniProtKB: P25440
PHAROS: P25440 GTEx: ENSG00000204256
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
59E (Subject of Investigation/LOI) Query on 59E Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], G [auth B], J [auth C], L [auth D]	methyl [(4S)-6-(1H-indol-4-yl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]acetate C₂₃ H₂₁ N₅ O₃ RARZHTSXOQRRPR-IBGZPJMESA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
PG0 Query on PG0 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], H [auth C], I [auth C], K [auth D]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain K [auth D]