SMTL ID : 8b4v.1

X-ray structure of furin (PCSK3) in complex with benzamidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.1: 15 residues within 4Å: Chain A: S.146, W.147, G.148, P.149, D.151, W.184, A.185, S.186, G.187, N.188, D.199, T.202, T.260, S.261 Ligands: CA.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.185 Hydrogen bonds: A:D.199, A:D.199 BEN.2: 4 residues within 4Å: Chain A: G.190, R.191, H.193, W.221 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.193 Hydrogen bonds: A:G.190 Water bridges: A:G.190 pi-Stacking: A:H.193

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.67, D.70, D.72, D.74, R.118 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.67, A:D.72, H2O.8, H2O.8, H2O.16 CA.4: 8 residues within 4Å: Chain A: D.8, D.55, V.98, A.99, N.101, V.103, G.105, V.106 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.8, A:D.55, A:V.98, A:V.103, A:G.105 CA.5: 7 residues within 4Å: Chain A: D.151, G.187, D.194, C.196, D.199, E.224 Ligands: BEN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.194, A:E.224, A:E.224, H2O.5, H2O.14

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

NA.6: 5 residues within 4Å: Chain A: T.202, S.204, T.207, S.209, M.427 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.207, A:S.209, A:S.209 NA.7: 3 residues within 4Å: Chain A: P.401, S.437, G.438 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.437 NA.8: 3 residues within 4Å: Chain A: D.157, G.158, A.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.158, A:G.158 Water bridges: A:A.160

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain A: F.168, Y.206, K.342, Y.464 Ligand excluded by PLIP

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

DMS.10: 8 residues within 4Å: Chain A: V.156, D.157, R.391, D.419, G.420, F.421, N.422, W.424 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.422 DMS.11: 4 residues within 4Å: Chain A: V.219, A.301, N.302, S.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.302

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.12: 3 residues within 4Å: Chain A: L.178, N.280, T.336 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.280, A:N.280, A:T.336, A:T.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lange, R.W. et al., Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors. Chemmedchem (2024)

Release Date

2023-10-04

Peptides

Furin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Furin

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