SMTL ID : 5k32.1

PDE4D crystal structure in complex with small molecule inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.78, H.114, D.115, D.232 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.78, A:H.114, A:D.115, A:D.232, H2O.3, H2O.5 ZN.20: 5 residues within 4Å: Chain B: H.78, H.114, D.115, D.232 Ligands: MG.21 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.78, B:H.114, B:D.115, B:D.232, H2O.11, H2O.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.115 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.115, H2O.2, H2O.3, H2O.4, H2O.5, H2O.5 MG.21: 3 residues within 4Å: Chain B: D.115, E.144 Ligands: ZN.20 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.115, H2O.11, H2O.11, H2O.12, H2O.13, H2O.15

2 x 6Q2: 4-[(3-methoxyphenyl)amino]-2-phenyl-7,8-dihydro-1,6-naphthyridin-5(6H)-one(Non-covalent)

6Q2.3: 16 residues within 4Å: Chain A: Y.73, T.185, M.187, D.232, L.233, N.235, W.246, T.247, I.250, F.254, S.282, Q.283, F.286 Ligands: EDO.10, EDO.11, EDO.13 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.233, A:I.250, A:F.254, A:F.286 Hydrogen bonds: A:Y.73, A:N.235, A:Q.283 Water bridges: A:Y.73 pi-Stacking: A:H.74, A:F.254, A:F.286 6Q2.22: 16 residues within 4Å: Chain B: Y.73, T.185, M.187, D.232, L.233, N.235, W.246, T.247, I.250, F.254, S.282, Q.283, F.286 Ligands: EDO.30, EDO.31, EDO.32 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.233, B:I.250, B:I.250, B:F.254, B:F.254, B:F.286, B:F.286 Hydrogen bonds: B:N.235, B:Q.283 Water bridges: B:Y.73, B:Y.73 pi-Stacking: B:H.74, B:F.286

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

EDO.4: 5 residues within 4Å: Chain A: K.176, I.179, D.180 Chain B: N.138, D.139 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: N.123, Q.124, I.127 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: E.64, D.65, Y.67, A.69, N.76 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: N.29, A.69, N.75, N.76, I.77 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: V.88, S.91, T.92, D.305 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: F.152, F.163, R.171 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: H.74, H.118, G.120, V.121, S.122, E.253, F.254, Q.257 Ligands: 6Q2.3 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.282, G.285, F.286 Ligands: 6Q2.3 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: H.68, D.117, P.119, L.133 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: M.187 Ligands: 6Q2.3 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: A.97, V.98 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: P.93, A.94, S.209, G.210, H.303, P.304, D.305 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain A: L.213 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.280, W.319, Y.320, T.323 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: F.21, E.25, I.77, R.249 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: L.183, A.184, K.189 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: R.244, E.280, W.319, Y.320, T.323 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: F.152, L.155, F.163, R.171, R.175 Ligands: EDO.25 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: R.171, Q.172 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: K.176, I.179, D.180 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: L.240, D.315, N.316 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain B: M.191, A.195, K.198 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: V.284, G.285, D.288, Y.289 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain B: H.74, H.118, G.120, V.121, S.122, E.253, F.254, Q.257 Ligands: 6Q2.22 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: S.282, G.285, F.286, I.290 Ligands: 6Q2.22 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: M.187, F.254, F.286 Ligands: 6Q2.22 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: V.150, K.153, L.154 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: H.68, D.117, P.119, L.133 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: T.207, S.208, V.211 Ligand excluded by PLIP EDO.36: 1 residues within 4Å: Chain B: T.207 Ligand excluded by PLIP EDO.37: 1 residues within 4Å: Chain B: N.29 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: E.96, A.97, V.98, F.99, I.104 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roberts, R.S. et al., 4-Amino-7,8-dihydro-1,6-naphthyridin-5(6 H)-ones as Inhaled Phosphodiesterase Type 4 (PDE4) Inhibitors: Structural Biology and Structure-Activity Relationships. J. Med. Chem. (2018)

Release Date

2017-03-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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