9DTW | pdb_00009dtw

Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4

• PDB DOI: https://doi.org/10.2210/pdb9DTW/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• 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: 1.39 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.98 kDa 
• Atom Count: 3,052 
• Modeled Residue Count: 342 
• Deposited Residue Count: 354 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteridine reductase	A	245	Homo sapiens	Mutation(s): 0  Gene Names: QDPR, DHPR, SDR33C1 EC: 1.5.1.34
UniProt & NIH Common Fund Data Resources
Find proteins for P09417 (Homo sapiens) Explore P09417  Go to UniProtKB:  P09417
PHAROS:  P09417 GTEx:  ENSG00000151552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	B	109	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BB9 (Subject of Investigation/LOI)	E [auth B]	(2S)-N-[(2R)-1-({[(1R)-6-(4-[(4S)-5,6-dihydro[1,2,4]triazolo[1,5-a]pyrazin-7(8H)-yl]-6-{[(1S)-3-methyl-1-(1H-1,2,4-triazol-3-yl)butyl]amino}-1,3,5-triazin-2-yl)-6-azaspiro[2.5]octan-1-yl]methyl}amino)-4-(4-methoxyphenyl)-1-oxobutan-2-yl]-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carboxamide C47 H67 N15 O5 SCOIQHVFHXASTM-RKKBZCJMSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.937	α = 90
b = 61.416	β = 90
c = 69.971	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