9R5N | pdb_00009r5n

FKBP12 in complex with binfunctional ligand b3c and the first bromodomain of BRD4

• PDB DOI: https://doi.org/10.2210/pdb9R5N/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2025-05-09 Released: 2026-05-20 
• Deposition Author(s): Meyners, C., Hausch, F.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.312 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.255 (DCC) 

Starting Models: experimental

Literature

Cell type-selective targeting by heterobifunctional protein binders via in-cell enrichment.

Bulldan, A., Zheng, M., Meyners, C., Purder, P.L., Krieger, J., Dreizler, J.K., Geiger, T.M., Repity, M.L., Lein, M.H., Quist-Lokken, I., Tewes, N., Smith, E.R., Schwab, K., Fischer, M., Schwalm, M.P., Dey, R., Aswathaman Sivashanmugam, S., Schlesiger, S., Moniot, S., Knapp, S., Hartung, I.V., Holien, T., Loewer, A., Hausch, F.

(2026) Nat Commun 17

• PubMed: 42754590 
• DOI: https://doi.org/10.1038/s41467-026-77460-w
• Primary Citation Related Structures: 
  29QL, 9QW8, 9R5N


• PubMed Abstract: 
  

  Non-catalytic heterobifunctional protein binders promise to expand the range of therapeutic options by establishing complexes between key target proteins and accessory presenter proteins equipped with additional properties. Here, we systematically investigate the rational design of such molecules, explore the biochemical basis of complex formation and determine how they achieve cellular efficacy using the endogenously expressed immunophilin FKBP12 as presenter protein and the transcriptional regulator BRD4 as target protein. We present classes of bifunctional molecules that enable selective, FKBP12-dependent killing of specific cell types at subnanomolar concentrations and allow to differentiate between closely related bromodomains of the BET family. We propose that the strongly potentiated efficacy of these bifunctional compounds is based on cellular enrichment through binding to the highly abundant presenter protein FKBP12, a mechanism we term "CellTrap". Our findings substantiate the concept that highly expressed, non-essential proteins can be repurposed as selective recruiters to expand therapeutic windows of existing small-molecule inhibitors, opening new avenues for designing targeted drugs with improved cell-type specificity.

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Organizational Affiliation: 
• Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
Vetter Pharma, Ravensburg, Germany.
Medicinal Chemistry & Drug Design, Global Research & Development, Merck Healthcare KGaA, Darmstadt, Germany.
Boehringer Ingelheim Vetmedica GmbH, Ingelheim a.R., Germany.
Institute of Structural Biology, University of Bonn, Germany.
Department of Immunology and Transfusion Medicine, St. Olav's University Hospital, Trondheim, Norway.
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology - NTNU, Trondheim, Norway.
Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany.
Institute of Medical Biochemistry, Medical Faculty, Otto von Guericke University, Magdeburg, Germany.
Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany.
Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
German Consortium for Translational Cancer research (DKTK) partner site Frankfurt/Mainz, Frankfurt am Main, Germany.
Biomolecule Analytics & Proteomics, Site Management Lab Services, Merck KGaA, Darmstadt, Germany.
Department of Biomedical Laboratory Science, Norwegian University of Science and Technology - NTNU, Trondheim, Norway.
Department of Biology, Technical University of Darmstadt, Darmstadt, Germany. [e-mail].
Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany. [e-mail].
Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany. [e-mail].
Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany. [e-mail].
Institute of Pharmaceutical and Biomedical Science (IPBS), Johannes Gutenberg University, Mainz, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.03 kDa 
• Atom Count: 3,413 
• Modeled Residue Count: 421 
• Deposited Residue Count: 468 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A, B	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	C, D	107	Homo sapiens	Mutation(s): 1  Gene Names: FKBP1A, FKBP1, FKBP12 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JCU (Subject of Investigation/LOI)	E [auth A], F [auth B]	~{tert}-butyl 2-[(9~{S})-7-[4-[3-[2-[2-[4-[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-2-oxidanylidene-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-5-yl]-1,2,3-triazol-1-yl]ethoxy]ethanoylamino]prop-1-ynyl]phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate C52 H55 Cl2 N11 O7 S2 QSOQNXPCLMYGFL-WFSSXJPUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.312 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.255 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.817	α = 90
b = 90.513	β = 90
c = 103.116	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoXDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Meyners, C., Hausch, F.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	--

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Database references