SMTL ID : 6ra1.1

Human Cyclophilin D in complex with norbornane fragment derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x JWB: 2-[(1~{R},2~{R},6~{S},7~{S})-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]decan-4-yl]ethanoic acid(Non-covalent)

JWB.1: 10 residues within 4Å: Chain A: R.54, F.59, M.60, Q.62, A.100, N.101, F.112, L.121, H.125 Ligands: JVQ.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.59, A:F.112, A:F.112, A:F.112, A:L.121 Hydrogen bonds: A:Q.62, A:Q.62, A:N.101 Water bridges: A:R.54, A:R.54 Salt bridges: A:R.54

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.2: 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: JWB.1 6 PLIP interactions: 6 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

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: S.58, F.59, W.120 No protein-ligand interaction detected (PLIP)

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

PG4.4: 6 residues within 4Å: Chain A: F.45, K.75, S.76, I.77, Y.78, G.79 No protein-ligand interaction detected (PLIP)

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

SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: H.53, R.54, N.70, G.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.53 Water bridges: A:R.150 Salt bridges: A:R.54

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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