SMTL ID : 7thf.1

Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B53

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x I4R: 3-(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-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-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)pentanedioic acid(Non-covalent)

I4R.1: 24 residues within 4Å: Chain A: R.54, F.59, M.60, Q.62, N.70, G.71, T.72, G.73, G.74, K.75, S.76, S.80, R.81, A.100, N.101, A.102, T.106, N.107, G.108, Q.110, F.112, W.120, L.121, H.125 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.72, A:R.81, A:A.100, A:A.102, A:L.121 Hydrogen bonds: A:R.54, A:R.54, A:Q.62, A:G.71, A:S.76, A:S.76, A:S.76, A:N.101, A:W.120 Water bridges: A:R.54, A:R.54, A:K.75, A:R.81 Salt bridges: A:K.75 pi-Stacking: A:F.112, A:H.125

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
A

Peptidyl-prolyl cis-trans isomerase F, mitochondrial

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