SMTL ID : 8syc.1

Crystal structure of PDE3B in complex with GSK4394835A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: H.89, H.169, D.170, D.285 Ligands: MG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.89, A:H.169, A:D.170, H2O.1, H2O.1 MG.2: 3 residues within 4Å: Chain A: D.170 Ligands: MG.1, X5W.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.170, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 7 residues within 4Å: Chain B: H.85, H.89, H.169, D.170, D.285 Ligands: MG.5, X5W.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.89, B:H.169, B:D.170, B:D.285, H2O.2 MG.5: 3 residues within 4Å: Chain B: D.170 Ligands: MG.4, X5W.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.170, H2O.2, H2O.2, H2O.2, H2O.3

2 x X5W: [3-[(4,7-dimethoxyquinolin-2-yl)carbonylamino]-5-[methyl-(phenylmethyl)carbamoyl]phenyl]-oxidanyl-oxidanylidene-boron(Covalent)(Non-covalent)

X5W.3: 19 residues within 4Å: Chain A: Y.84, H.85, D.170, H.173, L.198, E.199, D.285, N.287, G.288, P.289, H.296, W.299, T.300, I.303, F.307, L.335, Q.336, F.339 Ligands: MG.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.84, A:W.299, A:I.303 Hydrogen bonds: A:G.288 pi-Stacking: A:F.339 X5W.6: 20 residues within 4Å: Chain B: Y.84, H.85, H.89, D.170, H.173, E.179, L.243, N.287, G.288, P.289, H.296, W.299, T.300, I.303, F.307, L.335, Q.336, F.339 Ligands: MG.4, MG.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.84, B:L.243, B:W.299, B:I.303 Hydrogen bonds: B:G.288, B:Q.336 Water bridges: B:Y.84, B:Y.84, B:E.199, B:E.199, B:L.243 pi-Stacking: B:F.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rowley, A.M. et al., Discovery and SAR Study of Boronic Acid-Based Selective PDE3B Inhibitors from a Novel DNA-Encoded Library. J.Med.Chem. (2024)

Release Date

2024-02-07

Peptides

cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B