SMTL ID : 7ogi.1

Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.01 Å

Oligo State

monomer

Ligands

1 x VDH: N-(5-ethyl-4-oxidanylidene-1,2,3,6-tetrahydro-1,5-benzodiazocin-8-yl)-7-methyl-2-oxidanylidene-1H-pyrazolo[1,5-a]pyrimidine-6-carboxamide(Non-covalent)

VDH.1: 18 residues within 4Å: Chain A: H.54, R.55, Q.63, G.72, T.73, G.74, G.75, S.81, R.82, A.101, N.102, A.103, T.107, N.108, G.109, S.110, Q.111 Ligands: DMS.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:R.55, A:R.82, A:A.101 Hydrogen bonds: A:H.54, A:R.55, A:Q.63, A:G.72, A:R.82, A:R.82, A:N.102, A:Q.111 Water bridges: A:R.55, A:R.55, A:G.74, A:G.75, A:Q.111 pi-Cation interactions: A:R.55

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 10 residues within 4Å: Chain A: R.55, F.60, M.61, Q.63, A.101, N.102, F.113, L.122, H.126 Ligands: VDH.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.55, A:R.55 pi-Cation interactions: A:F.113

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

PG4.3: 6 residues within 4Å: Chain A: V.93, G.94, P.95, G.96, V.97, H.131 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva, D.O. et al., Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide. To Be Published

Release Date

2022-06-01

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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