SMTL ID : 6r8o.1

Human Cyclophilin D in complex with 1-(((2R,3S,6R)-3-hydroxy-2,3,4,6-tetrahydro-1H-2,6-methanobenzo[c][1,5]oxazocin-8-yl)methyl)-3-(2-((R)-2-(2-(methylthio)phenyl)pyrrolidin-1-yl)-2-oxoethyl)urea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 4 residues within 4Å: Chain A: V.92, G.93, P.94, H.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.92 Water bridges: A:H.130

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: E.133, G.134, M.135, D.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.134, A:M.135, A:D.136 Water bridges: A:D.136

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: S.146, K.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.147 Water bridges: A:S.148

1 x JV2: 1-(((2R,3S,6R)-3-hydroxy-2,3,4,6-tetrahydro-1H-2,6-methanobenzo[c][1,5]oxazocin-8-yl)methyl)-3-(2-((R)-2-(2-(methylthio)phenyl)pyrrolidin-1-yl)-2-oxoethyl)urea(Non-covalent)

JV2.4: 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, T.106, G.108, Q.110, F.112, L.121, H.125 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.59, A:F.112, A:L.121 Hydrogen bonds: A:R.54, A:Q.62, A:S.80, A:R.81, A:N.101, A:N.101, A:N.101, A:T.106 Water bridges: A:R.54, A:R.54, A:R.54, 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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