SMTL ID : 4htx.2 (1 other biounit)

Crystal structure of PDE2 catalytic domain in complex with BAY60-7550

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.83, H.119, D.120, D.231 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.83, A:H.119, A:D.120, A:D.231, H2O.2, H2O.5 ZN.4: 5 residues within 4Å: Chain B: H.83, H.119, D.120, D.231 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.83, B:H.119, B:D.120, B:D.231, H2O.8, H2O.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.120, T.191 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.1, H2O.1, H2O.5 MG.5: 3 residues within 4Å: Chain B: D.120, T.191 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.120, H2O.8, H2O.8, H2O.8, H2O.13, H2O.13

2 x 19F: 2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one(Non-covalent)

19F.3: 18 residues within 4Å: Chain A: Y.78, H.79, T.191, L.193, H.196, T.228, L.232, Q.235, I.249, Y.250, F.253, M.270, L.281, Q.282, S.284, F.285, I.289, I.293 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.78, A:L.193, A:H.196, A:T.228, A:L.232, A:I.249, A:F.253, A:F.285, A:F.285, A:F.285, A:I.289, A:I.293 Hydrogen bonds: A:Q.235, A:Q.282, A:Q.282 pi-Stacking: A:F.285 19F.6: 18 residues within 4Å: Chain B: Y.78, H.79, T.191, L.193, H.196, T.228, L.232, Q.235, I.249, Y.250, F.253, M.270, L.281, Q.282, S.284, F.285, I.289, I.293 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.78, B:L.193, B:H.196, B:T.228, B:L.232, B:Q.235, B:F.253, B:F.285, B:F.285, B:F.285, B:I.289, B:I.293 Hydrogen bonds: B:Q.235, B:Q.282, B:Q.282 Water bridges: B:Y.78 pi-Stacking: B:F.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, J. et al., X-ray Crystal Structure of Phosphodiesterase 2 in Complex with a Highly Selective, Nanomolar Inhibitor Reveals a Binding-Induced Pocket Important for Selectivity. J.Am.Chem.Soc. (2013)

Release Date

2013-08-28

Peptides

cGMP-dependent 3',5'-cyclic phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

cGMP-dependent 3',5'-cyclic phosphodiesterase

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