9LYG | pdb_00009lyg

Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201

• PDB DOI: https://doi.org/10.2210/pdb9LYG/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-20 Released: 2025-03-26 
• Deposition Author(s): Kato, S., Tsuchikawa, H., Katoh, A., Matsuoka, S., Sugiyama, S.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.188 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201

Kato, S., Tsuchikawa, H., Katoh, A., Matsuoka, S., Sugiyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 12.91 kDa 
• Atom Count: 1,181 
• Modeled Residue Count: 107 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	111	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L7S (Subject of Investigation/LOI)	B [auth A]	5-[(2~{S})-1-cyclohexylsulfonylpiperidin-2-yl]-3-[3-(3,4-dimethoxyphenyl)propyl]-1,2,4-oxadiazole C24 H35 N3 O5 S RPFKIQSMYIANNB-FQEVSTJZSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.188 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.577	α = 90
b = 48.039	β = 90
c = 65.306	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Kato, S., Tsuchikawa, H., Katoh, A., Matsuoka, S., Sugiyama, S.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	23ak0101198h0001

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release