SMTL ID : 6r8w.1

Human Cyclophilin D in complex with 2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x O4B: 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE(Non-covalent)

O4B.1: 5 residues within 4Å: Chain A: I.56, S.58, F.59, W.120, K.147 No protein-ligand interaction detected (PLIP)

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 5 residues within 4Å: Chain A: V.92, G.93, P.94, V.96, H.130 No protein-ligand interaction detected (PLIP)

1 x JVH: 2-(exo-3,5-Dioxo-4-aza-tricyclo[5.2.1.02,6]dec-4-yl)-N-((1R,9R,10S)-10-hydroxy-12-oxa-8-aza-tricyclo[7.3.1.02,7]trideca-2(7),3,5-trien-4-ylmethyl)-acetamide(Non-covalent)

JVH.3: 18 residues within 4Å: Chain A: R.54, F.59, M.60, Q.62, G.71, T.72, G.73, G.74, S.80, R.81, A.100, N.101, A.102, T.106, G.108, Q.110, F.112, H.125 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.59, A:A.100, A:F.112, A:F.112 Hydrogen bonds: A:R.54, A:R.54, A:Q.62, A:S.80, A:R.81, A:N.101, A:N.101, A:T.106 Water bridges: A:Q.110, A:Q.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gradler, U. et al., Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies. Bioorg.Med.Chem.Lett. (2019)

Release Date

2019-11-27

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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