7R2J | pdb_00007r2j

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

PDB DOI: https://doi.org/10.2210/pdb7R2J/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: 1.26 Å
R-Value Free:
0.166 (Depositor), 0.170 (DCC)
R-Value Work:
0.140 (Depositor), 0.150 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 7R2L

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: 18.14 kDa
Atom Count: 1,587
Modeled Residue Count: 164
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V0Z (Subject of Investigation/LOI) Query on V0Z 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]	N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide C₁₄ H₁₃ N₅ O₂ DTFXMPJTNSKHJT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS (Subject of Investigation/LOI) Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.166 (Depositor), 0.170 (DCC)
R-Value Work: 0.140 (Depositor), 0.150 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.059	α = 90
b = 56.059	β = 90
c = 85.851	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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

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.