SMTL ID : 7thd.1

Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B52

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

1 x I4V: [(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)methyl]propanedioic acid(Non-covalent)

I4V.1: 25 residues within 4Å: Chain A: R.53, F.58, M.59, Q.61, N.69, G.70, T.71, G.72, G.73, K.74, S.75, G.78, S.79, R.80, A.99, N.100, A.101, T.105, N.106, G.107, Q.109, F.111, W.119, L.120, H.124 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.71, A:R.80, A:A.99, A:A.101, A:L.120 Hydrogen bonds: A:R.53, A:R.53, A:Q.61, A:G.70, A:S.75, A:R.80, A:N.100, A:W.119 Water bridges: A:R.53, A:R.53, A:K.74, A:K.74, A:G.78 Salt bridges: A:K.74 pi-Stacking: A:F.111, A:H.124

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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