SMTL ID : 7qy2.1

X-ray structure of furin in complex with the dichlorophenylpyridine-based inhibitor 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x I0Q: (2R)-4-[4-[5-[4-[[4-(acetamidomethyl)piperidin-1-ium-1-yl]methyl]-6-[3,5-bis(chloranyl)phenyl]pyridin-2-yl]oxypyrimidin-2-yl]piperazin-1-ium-1-yl]-2-methyl-butanoate(Non-covalent)

I0Q.1: 23 residues within 4Å: Chain A: L.45, D.47, D.84, R.86, H.87, M.119, L.120, V.124, T.125, D.126, E.129, L.133, A.145, S.146, W.147, G.148, P.149, D.157, G.158, P.159, A.160, W.184, Y.201 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.120, A:E.129, A:A.160, A:W.184, A:Y.201 Hydrogen bonds: A:Y.201 Water bridges: A:R.86, A:R.86, A:D.126, A:D.126, A:W.147 Salt bridges: A:R.86, A:H.87, A:E.129, A:D.157 Halogen bonds: A:L.45

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.67, D.70, D.72, D.74, R.118 Ligands: DMS.14 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.67, A:D.72, H2O.5, H2O.9, H2O.15 CA.3: 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.4: 6 residues within 4Å: Chain A: D.151, G.187, D.194, C.196, D.199, E.224 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.194, A:E.224, H2O.5, H2O.9, H2O.12

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

NA.5: 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:T.207, A:S.209 NA.6: 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.7: 2 residues within 4Å: Chain A: T.306, N.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.306 NA.8: 5 residues within 4Å: Chain A: W.147, G.148, D.151, G.187, N.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.148, A:P.149

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

6 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: 6 residues within 4Å: Chain A: F.168, V.171, S.172, Y.206, W.283, Q.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.206 Water bridges: A:Q.340 DMS.12: 8 residues within 4Å: Chain A: W.147, N.188, W.221, Y.222, T.258, G.259, T.260, S.261 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.188 DMS.13: 2 residues within 4Å: Chain A: Y.79, R.250 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.76, A:Y.79, A:R.250 pi-Cation interactions: A:Y.79 DMS.14: 6 residues within 4Å: Chain A: Q.76, P.77, R.78, Y.79, R.118 Ligands: CA.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.70 DMS.15: 4 residues within 4Å: Chain A: V.219, A.301, N.302, S.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.302 Salt bridges: A:D.303

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

NAG.16: 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:N.280, A:T.336

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dahms, S.O. et al., Dichlorophenylpyridine-Based Molecules Inhibit Furin through an Induced-Fit Mechanism. Acs Chem.Biol. (2022)

Release Date

2022-04-20

Peptides

Furin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Furin

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