SMTL ID : 7o1y.1

X-ray structure of furin in complex with the guanylhydrazone-based inhibitor 2 (mi307) soaked at 0.25 M NaCl

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

3 x UYQ: [[(2E)-2-[[4-[(E)-[[azaniumylidene(azanyl)methyl]hydrazinylidene]methyl]phenyl]methylidene]hydrazinyl]-azanyl-methylidene]azanium(Non-covalent)

UYQ.1: 18 residues within 4Å: Chain A: D.46, D.47, D.84, N.85, H.87, L.120, S.146, W.147, G.148, P.149, E.150, D.151, W.184, A.185, G.187, D.199 Ligands: UYQ.2, DMS.16 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.84, A:H.87, A:S.146, A:G.148, A:P.149, A:P.149 Water bridges: A:D.84, A:W.184 Salt bridges: A:D.46, A:D.47, A:D.151, A:D.199 UYQ.2: 14 residues within 4Å: Chain A: L.120, D.121, V.124, E.129, W.147, G.148, P.149, E.150, D.157, G.158, P.159, A.160, Y.201 Ligands: UYQ.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.120, A:V.124 Hydrogen bonds: A:L.120, A:Y.201, A:Y.201 Water bridges: A:E.150 Salt bridges: A:E.129, A:D.157 UYQ.3: 6 residues within 4Å: Chain A: D.157, G.158, P.159, A.160, R.161, E.164 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.161 Hydrogen bonds: A:R.161 Water bridges: A:V.156, A:D.157, A:G.158 Salt bridges: A:D.157

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.7, H2O.8, H2O.15 CA.5: 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.6: 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.3, H2O.9, H2O.10

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

NA.7: 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.202, A:T.207, A:S.209 NA.8: 2 residues within 4Å: Chain A: T.306, N.307 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.306, A:M.402, A:M.402, A:T.404

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

CL.9: 3 residues within 4Å: Chain A: Y.206, K.342, Y.464 Ligand excluded by PLIP

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

DMS.10: 9 residues within 4Å: Chain A: V.156, D.157, R.391, D.419, G.420, F.421, N.422, W.424 Ligands: DMS.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.422 DMS.11: 5 residues within 4Å: Chain A: 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: 2 residues within 4Å: Chain A: Y.79, R.250 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.76, A:R.250 pi-Cation interactions: A:Y.79 DMS.13: 7 residues within 4Å: Chain A: N.188, W.221, Y.222, T.258, G.259, T.260 Ligands: DMS.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.258 Water bridges: A:N.188, A:S.261 DMS.14: 4 residues within 4Å: Chain A: D.70, Q.76, R.78, R.118 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.302 DMS.16: 5 residues within 4Å: Chain A: H.87, N.188, S.261 Ligands: UYQ.1, DMS.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.261 Water bridges: A:S.146, A:S.261 pi-Cation interactions: A:H.87 DMS.17: 8 residues within 4Å: Chain A: T.385, L.386, S.387, D.419, G.420, F.421, N.422 Ligands: DMS.10 No protein-ligand interaction detected (PLIP)

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

NAG.18: 3 residues within 4Å: Chain A: L.178, N.280, T.336 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.280, A:N.280, A:N.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dahms, S.O. et al., OFF-State-Specific Inhibition of the Proprotein Convertase Furin. Acs Chem.Biol. (2021)

Release Date

2021-09-01

Peptides

Furin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Furin

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