7R2I | pdb_00007r2i

Human Cyclophilin D in complex with fragment

PDB DOI: https://doi.org/10.2210/pdb7R2I/pdb

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

Deposited: 2022-02-04 Released: 2023-02-15
Deposition Author(s): Silva, D.O., Graedler, U., Bandeiras, T.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free:
0.179 (Depositor), 0.164 (DCC)
R-Value Work:
0.140 (Depositor)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7R2I

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7R2J 7R2L 7ZDN

Literature

Structure-based design of pyrazole derivatives targeting the human Cyclophilin D binding site

Silva, D.O., Freitas, M.C., Malta, C.F., Martins, M.T., Sousa, P.M., Matias, P.M., Schwarz, D., Ventura, M.R., Gradler, U., Bandeiras, T.M.

(2026) Int J Biol Macromol : 151496

DOI: https://doi.org/10.1016/j.ijbiomac.2026.151496

Macromolecule Content

Total Structure Weight: 18.32 kDa
Atom Count: 1,606
Modeled Residue Count: 164
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE (Subject of Investigation/LOI) Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
UPZ (Subject of Investigation/LOI) Query on UPZ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ethyl 7-methyl-2-oxidanylidene-1,3-dihydropyrazolo[1,5-a]pyrimidine-6-carboxylate C₁₀ H₁₁ N₃ O₃ UGSAIASUGJTLIZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
DMS (Subject of Investigation/LOI) Query on DMS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.179 (Depositor), 0.164 (DCC)
R-Value Work: 0.140 (Depositor)
R-Value Observed: 0.141 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.837	α = 90
b = 56.837	β = 90
c = 87.426	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Bandeiras, T.M.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2026-04-01
Changes: Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.