SMTL ID : 6r9s.1

Human Cyclophilin D in complex with bicyclic fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x JVN: (1~{R},9~{R},10~{S})-4-fluoranyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol(Non-covalent)

JVN.1: 13 residues within 4Å: Chain A: G.71, T.72, G.73, G.74, S.80, R.81, A.100, N.101, A.102, T.106, G.108, Q.110 Ligands: JVN.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.81, A:R.81 Water bridges: A:A.100, A:G.108, A:Q.110 JVN.2: 4 residues within 4Å: Chain A: T.72, R.81, A.102 Ligands: JVN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.81 Water bridges: A:R.81, A:A.102 Halogen bonds: A:T.72

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 10 residues within 4Å: Chain A: R.54, I.56, F.59, M.60, Q.62, A.100, F.112, L.121, H.125, S.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.54, A:R.54, A:Q.62 Water bridges: A:S.148

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

PG4.4: 5 residues within 4Å: Chain A: V.92, G.93, P.94, V.96, H.130 No protein-ligand interaction detected (PLIP)

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

SO4.5: 4 residues within 4Å: Chain A: E.133, G.134, M.135, D.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.134, A:M.135, A:D.136, A:D.136 Water bridges: A:D.136

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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