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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.190 (Depositor), 0.192 (DCC)
R-Value Work:
0.142 (Depositor), 0.144 (DCC)
R-Value Observed:
0.144 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4J5A

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 18.14 kDa
Atom Count: 1,561
Modeled Residue Count: 164
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

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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
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
67Z Query on 67Z Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	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		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.190 (Depositor), 0.192 (DCC)
R-Value Work: 0.142 (Depositor), 0.144 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-02-19

Deposition Author(s):

Revision History (Full details and data files)

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

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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.