7PMT

Human Cyclophilin D in complex with N-[(5-ethyl-4-oxo-1,2,3,4,5,6- hexahydro-1,5-benzodiazocin-8-yl)methyl]-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb7PMT/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2021-09-02 Released: 2022-09-14 
• Deposition Author(s): Silva, D.O., Graedler, U., Bandeiras, T.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.148 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7ZDN

Literature

Human Cyclophilin D in complex with N-[(4-aminophenyl)methyl]-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide

Silva, D.O., Graedler, U.

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: 18.27 kDa 
• Atom Count: 1,585 
• Modelled Residue Count: 164 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A	165	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7UO (Subject of Investigation/LOI)	C [auth A]	~{N}-[(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)methyl]-7-methyl-2-oxidanylidene-1,3-dihydropyrazolo[1,5-a]pyrimidine-6-carboxamide C21 H25 N6 O3 LHEOUBYGNUOQPC-UHFFFAOYSA-O
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 0.148 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.153	α = 90
b = 57.153	β = 90
c = 87.703	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Silva, D.O., Graedler, U., Bandeiras, T.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description