SMTL ID : 5nwo.1

Scaffold-ligand complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x 9CK: 1-[(4-aminophenyl)methyl]-3-[2-[2-(2-bromophenyl)pyrazolidin-1-yl]-2-oxidanylidene-ethyl]urea(Non-covalent)

9CK.1: 14 residues within 4Å: Chain A: R.55, F.60, M.61, Q.63, G.72, G.74, A.101, N.102, T.107, G.109, Q.111, F.113, L.122, H.126 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.113, A:L.122 Hydrogen bonds: A:R.55, A:Q.63, A:N.102, A:N.102, A:N.102, A:T.107 Water bridges: A:R.55, A:R.55, A:Q.111 pi-Stacking: A:F.60

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: N.13, K.15, K.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.15, A:K.154 EDO.3: 4 residues within 4Å: Chain A: R.37, Q.163, S.165 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.163 Water bridges: A:R.37 EDO.4: 3 residues within 4Å: Chain A: Q.163, S.165 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.163 EDO.5: 4 residues within 4Å: Chain A: R.19, V.21, E.134, L.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.19 EDO.6: 3 residues within 4Å: Chain A: E.134, G.135, D.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.135, A:M.136, A:D.137

2 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.7: 4 residues within 4Å: Chain A: V.93, G.94, P.95, H.131 No protein-ligand interaction detected (PLIP) 12P.8: 5 residues within 4Å: Chain A: G.50, T.52, H.70, K.155, V.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.155

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

PO4.9: 2 residues within 4Å: Chain A: S.147, K.148 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.148 Water bridges: A:S.149

3 x NA: SODIUM ION(Non-functional Binders)

NA.10: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.106 NA.11: 1 residues within 4Å: Chain A: F.60 No protein-ligand interaction detected (PLIP) NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zacharchenko, T. et al., Human Cyclophilin D Complexed with Inhibitor. To Be Published

Release Date

2018-05-30

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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