9RLM | pdb_00009rlm

HUMAN CYCLOPHILIN D IN COMPLEX WITH INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb9RLM/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-06-17 Released: 2025-07-02 
• Deposition Author(s): Graedler, U.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.206 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

HUMAN CYCLOPHILIN D IN COMPLEX WITH INHIBITOR

Graedler, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.47 kDa 
• Atom Count: 1,519 
• Modeled Residue Count: 164 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A	164	Homo sapiens	Mutation(s): 1  Gene Names: PPIF, CYP3 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens) Explore P30405  Go to UniProtKB:  P30405
PHAROS:  P30405 GTEx:  ENSG00000108179

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JG4 (Subject of Investigation/LOI)	B [auth A]	~{N}'-cyclopentyl-~{N}-[2-[(1~{R},9~{R},10~{S})-10-oxidanyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-4-yl]ethyl]ethanediamide C20 H27 N3 O4 TWJNDXFEOOUBGG-KZNAEPCWSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.206 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.039	α = 90
b = 57.039	β = 90
c = 114.404	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Graedler, U.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release