SMTL ID : 6r9u.1

Human Cyclophilin D in complex with fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.26 Å

Oligo State

monomer

Ligands

1 x JVQ: 14-ethyl-4,6-dioxa-10,14-diazatricyclo[7.6.0.0^{3,7}]pentadeca-1(9),2,7-trien-13-one(Non-covalent)

JVQ.1: 12 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.102 Hydrogen bonds: A:R.81, A:T.106, A:Q.110 Water bridges: A:Q.62, A:S.109, A:Q.110

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

SO4.2: 2 residues within 4Å: Chain A: S.146, K.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.147 Water bridges: A:S.146, A:S.148

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 2 residues within 4Å: Chain A: F.59 Ligands: PGE.6 No protein-ligand interaction detected (PLIP) PGE.5: 5 residues within 4Å: Chain A: G.49, T.51, H.69, K.154, V.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.154 Water bridges: A:T.51 PGE.6: 8 residues within 4Å: Chain A: F.59, M.60, Q.62, A.100, F.112, L.121, H.125 Ligands: PGE.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.62 Water bridges: A:Q.62

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)

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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