› 6ra1

X-ray diffraction
2Å resolution

Human Cyclophilin D in complex with norbornane fragment derivative

Released:
DOI: 10.2210/pdb6ra1/pdb
PDB entry 6ra1 coloured by chain, front view.
PDB entry 6ra1 coloured by chain, side view.
PDB entry 6ra1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies.
Grädler U, Schwarz D, Blaesse M, Leuthner B, Johnson TL, Bernard F, Jiang X, Marx A, Gilardone M, Lemoine H, Roche D, Jorand-Lebrun C
Bioorg Med Chem Lett 29 126717 (2019)
PMID: 31635932

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151715 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidyl-prolyl cis-trans isomerase F, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 164 amino acids
Theoretical weight: 17.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P30405 (Residues: 44-207; Coverage: 79%)
Gene names: CYP3, PPIF
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

Ligands and Environments

5 bound ligands:
Ligand JWB 1 x JWB
Ligand JVQ 1 x JVQ
Ligand PEG 1 x PEG
Ligand PG4 1 x PG4
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P43212
Unit cell:
a: 56.889Å b: 56.889Å c: 116.147Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.192 0.226
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Concepts and Core Principles of Fragment-Based Drug Design.
Kirsch et al. (2019)
1 more

2 mentions without citation

Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies.
Grädler et al. (2019)
1 more