SMTL ID : 6boj.5 (4 other biounits)

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.1, H2O.7 ZN.4: 1 residues within 4Å: Chain A: H.76 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.76, H2O.1, H2O.10, H2O.11, H2O.23 ZN.6: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.7 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.124, B:D.125, B:D.242, H2O.13, H2O.17 ZN.11: 5 residues within 4Å: Chain C: H.88, H.124, D.125, D.242 Ligands: MG.12 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.88, C:H.124, C:D.125, C:D.242, H2O.24, H2O.29 ZN.16: 5 residues within 4Å: Chain D: H.88, H.124, D.125, D.242 Ligands: MG.17 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.88, D:H.124, D:D.125, D:D.242, H2O.36, H2O.40 ZN.19: 1 residues within 4Å: Chain D: H.76 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:H.76, H2O.12, H2O.35, H2O.42, H2O.43

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.4, H2O.4, H2O.6, H2O.9 MG.7: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.13, H2O.14, H2O.17, H2O.18, H2O.19 MG.12: 2 residues within 4Å: Chain C: D.125 Ligands: ZN.11 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.125, H2O.24, H2O.25, H2O.26, H2O.28, H2O.31 MG.17: 2 residues within 4Å: Chain D: D.125 Ligands: ZN.16 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.125, H2O.36, H2O.37, H2O.38, H2O.40, H2O.41

4 x E31: 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide(Non-covalent)

E31.3: 17 residues within 4Å: Chain A: H.84, S.132, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296, F.357, I.358, T.361 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.243, A:N.245, A:Y.253, A:I.260, A:I.260, A:F.296, A:F.296, A:F.296, A:F.357, A:F.357, A:T.361 Hydrogen bonds: A:Q.293 Water bridges: A:H.84, A:V.131, A:S.132, A:S.132 pi-Stacking: A:F.296 E31.8: 18 residues within 4Å: Chain B: H.84, S.132, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296, F.357, I.358, T.361, F.362 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.243, B:N.245, B:Y.253, B:I.260, B:I.260, B:F.296, B:F.296, B:F.296, B:F.357, B:F.357, B:T.361, B:F.362 Hydrogen bonds: B:Q.293 Water bridges: B:V.131, B:S.132, B:S.132 pi-Stacking: B:F.296 E31.13: 18 residues within 4Å: Chain C: H.84, S.132, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296, F.357, I.358, T.361, F.362 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.243, C:N.245, C:Y.253, C:I.260, C:I.260, C:F.296, C:F.296, C:F.296, C:F.357, C:T.361, C:F.362 Hydrogen bonds: C:Q.293 Water bridges: C:V.131, C:S.132, C:S.132 pi-Stacking: C:F.296 E31.18: 19 residues within 4Å: Chain D: Y.83, H.84, S.132, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, F.264, M.281, S.292, Q.293, F.296, F.357, I.358, T.361, F.362 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.83, D:L.243, D:N.245, D:Y.253, D:I.260, D:F.296, D:F.296, D:F.296, D:F.357, D:F.357, D:T.361, D:F.362 Hydrogen bonds: D:Q.293 Water bridges: D:H.84, D:V.131, D:S.132, D:S.132 pi-Stacking: D:F.296

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

CL.5: 5 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: H.29, V.30, F.31, R.32, L.252 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: H.29, V.30, F.31, R.32, L.252 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: H.29, V.30, F.31, R.32, L.252 Ligand excluded by PLIP

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 3 residues within 4Å: Chain B: L.136, S.141, R.270 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.141, B:E.142, B:E.142, B:R.270 MPD.15: 1 residues within 4Å: Chain C: R.270 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Memory enhancing effects of BPN14770, an allosteric inhibitor of phosphodiesterase-4D, in wild-type and humanized mice. Neuropsychopharmacology (2018)

Release Date

2018-08-22

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

cAMP-specific 3',5'-cyclic phosphodiesterase 4D

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