4J5A | pdb_00004j5a

Human Cyclophilin D Complexed with an Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4J5A/pdb

• Classification: Isomerase/Isomerase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-08 Released: 2014-02-19 
• Deposition Author(s): Gelin, M., Colliandre, L., Bessin, Y., Guichou, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Rationnal Design of small-molecule inhibitors of human Cyclophilins and HCV replication.

Colliandre, L., Hamed-Belkacem, H., Gelin, M., Bessin, Y., Douguet, D., Bourguet, W., Pawlotsky, J.M., Guichou, J.F.

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)

Macromolecule Content

• Total Structure Weight: 18.14 kDa 
• Atom Count: 1,561 
• Modelled 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 [auth X]	164	Homo sapiens	Mutation(s): 1  Gene Names: CYP3, PPIF 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
67Z	B [auth X]	1-(4-aminobenzyl)-3-{2-[(2R)-2-(2,5-dimethoxyphenyl)pyrrolidin-1-yl]-2-oxoethyl}urea C22 H28 N4 O4 BLBIXVAZFDEMKW-LJQANCHMSA-N
DMS	C [auth X]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.09	α = 90
b = 57.09	β = 90
c = 88.07	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Gelin, M., Colliandre, L., Bessin, Y., Guichou, J.F.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations