9DU1 | pdb_00009du1

Co-crystal structure of the ternary complex of human FKBP12, BRD9 bromo domain and Compound 1

• PDB DOI: https://doi.org/10.2210/pdb9DU1/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-02 Released: 2025-10-08 
• Deposition Author(s): Romanowski, M.J., Viscomi, J.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Models: experimental

Literature

Ternary complex DNA-encoded library screening uncovers FKBP molecular glues

Zandi, T.A., Tan, Z.R., Romanowski, M.J., Viscomi, J.S., Tong, B.Q., Bonazzi, S., Zecri, F.J., Schreiber, S.L., Michaud, G.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 105.25 kDa 
• Atom Count: 7,707 
• Modeled Residue Count: 841 
• Deposited Residue Count: 900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A, B, C, D	109	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 9	E, F, G, H	116	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens) Explore Q9H8M2  Go to UniProtKB:  Q9H8M2
PHAROS:  Q9H8M2 GTEx:  ENSG00000028310

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BB8 (Subject of Investigation/LOI)	I [auth B], J [auth D], L [auth G], M [auth H]	4-[4-{cyclopropyl[(1-methyl-1H-pyrazol-4-yl)methyl]amino}-6-({1-[(2R)-2-{[(2S)-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carbonyl]amino}-4-(4-methoxyphenyl)butanoyl]piperidin-4-yl}amino)-1,3,5-triazin-2-yl]-N-ethylpiperazine-1-carboxamide C47 H69 N13 O6 ADQZIARRQDOKQN-AMAPPZPBSA-N
GOL	K [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.163	α = 90
b = 97.512	β = 93.69
c = 100.002	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Romanowski, M.J., Viscomi, J.S.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release