SMTL ID : 7th1.1

Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

monomer

Ligands

1 x I5J: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(3-methylphenyl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide(Non-covalent)

I5J.1: 23 residues within 4Å: Chain A: R.55, I.57, P.58, S.59, F.60, M.61, Q.63, N.71, G.72, T.73, G.74, R.82, A.101, N.102, A.103, T.107, N.108, G.109, Q.111, F.113, W.121, L.122, H.126 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.73, A:A.101, A:A.103, A:A.103, A:L.122 Hydrogen bonds: A:R.55, A:R.55, A:P.58, A:Q.63, A:G.72, A:N.102, A:W.121 Water bridges: A:R.55 pi-Stacking: A:F.113 pi-Cation interactions: A:H.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peterson, A.A. et al., Discovery and molecular basis of subtype-selective cyclophilin inhibitors. Nat.Chem.Biol. (2022)

Release Date

2022-08-24

Peptides

Peptidyl-prolyl cis-trans isomerase F, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Peptidyl-prolyl cis-trans isomerase F, mitochondrial