SMTL ID : 6cyc.1

PDE2 in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.150, D.151, D.262 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.114, A:H.150, A:D.151, A:D.262, H2O.1, H2O.4 ZN.10: 4 residues within 4Å: Chain B: H.114, H.150, D.151, D.262 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.114, B:H.150, B:D.151, B:D.262, H2O.8, H2O.12

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.151 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.151, H2O.1, H2O.1, H2O.2, H2O.3, H2O.5 MG.11: 1 residues within 4Å: Chain B: D.151 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.151, H2O.8, H2O.8, H2O.9, H2O.9, H2O.14

2 x FKJ: 3-(hydroxymethyl)-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione(Non-covalent)

FKJ.3: 18 residues within 4Å: Chain A: Y.109, H.110, T.222, D.223, L.224, T.259, D.262, L.263, Q.266, I.276, I.280, F.284, M.301, Q.313, F.316, I.324 Ligands: EDO.4, EDO.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.263, A:I.280 Hydrogen bonds: A:Q.266, A:Q.313, A:Q.313 Water bridges: A:Y.109, A:D.265 pi-Stacking: A:F.316 FKJ.12: 17 residues within 4Å: Chain B: Y.109, H.110, T.222, D.223, L.224, T.259, D.262, L.263, Q.266, I.276, I.280, F.284, Q.313, F.316, I.324 Ligands: EDO.13, EDO.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.263, B:I.280 Hydrogen bonds: B:Q.266 Water bridges: B:Y.109, B:D.265, B:Y.281, B:Q.313, B:Q.313 pi-Stacking: B:F.316

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: L.224, F.284, M.301, F.316 Ligands: FKJ.3, EDO.5, EDO.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.313 EDO.5: 6 residues within 4Å: Chain A: N.158, F.284, M.301, M.302 Ligands: EDO.4, EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.158 Water bridges: A:N.158, A:N.159, A:N.159 EDO.6: 6 residues within 4Å: Chain A: T.222, D.223, L.224 Ligands: FKJ.3, EDO.4, EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.222, A:L.224 Water bridges: A:N.159 EDO.7: 7 residues within 4Å: Chain A: S.175, E.176 Chain B: H.226, I.230, R.251, L.252, C.255 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.226, B:R.251, B:R.251, A:S.175 Water bridges: A:S.175 EDO.8: 3 residues within 4Å: Chain A: K.23, F.26, Q.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.23, A:Q.187 Water bridges: A:R.105 EDO.9: 7 residues within 4Å: Chain A: I.189, N.193, Y.208, L.212 Chain B: R.205, K.206, Q.209 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.193, A:Y.208, A:Y.208, B:R.205 EDO.13: 5 residues within 4Å: Chain B: T.222, D.223, L.224 Ligands: FKJ.12, EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.222, B:L.224 EDO.14: 7 residues within 4Å: Chain B: N.158, F.284, M.299, M.301, M.302 Ligands: EDO.13, EDO.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.158 Water bridges: B:N.159, B:N.159, B:S.160 EDO.15: 7 residues within 4Å: Chain B: L.224, F.284, M.301, F.316, I.320 Ligands: FKJ.12, EDO.14 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain B: N.53, T.58, Y.59, T.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.53, B:T.60, B:T.60 EDO.17: 4 residues within 4Å: Chain B: L.228, F.231, H.319, P.323 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stachel, S.J. et al., Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor. ACS Med Chem Lett (2018)

Release Date

2018-09-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

cGMP-dependent 3',5'-cyclic phosphodiesterase

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