SMTL ID : 6ft0.2 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-425

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.90, A:H.126, A:D.127, A:D.244, H2O.1, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.127, E.156 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.1, H2O.1, H2O.2, H2O.3, H2O.3

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

EDO.3: 5 residues within 4Å: Chain A: F.266, S.281, P.282, C.284 Ligands: E6E.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.269 EDO.4: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41, A:N.88, A:R.261 Water bridges: A:Y.79 EDO.5: 3 residues within 4Å: Chain A: K.188, I.191, D.192 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: E.170, N.171 Ligands: EPE.8 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: A.109, V.110, F.111, T.112 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: D.192, L.195, A.196, K.201, Q.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.192, A:Q.237 EDO.12: 4 residues within 4Å: Chain A: D.24, W.28, G.29, H.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.31 EDO.13: 1 residues within 4Å: Chain A: E.144 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 6 residues within 4Å: Chain A: P.64, D.66, T.67, N.171, Q.176 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.66 Water bridges: A:Q.176 EPE.11: 8 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, Q.253, L.254, Q.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.253, A:Q.257 Salt bridges: A:H.31, A:E.37, A:E.37

1 x E6E: 4-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-2-(1-{thieno[3,2-d]pyrimidin-4-yl}piperidin-4-yl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one(Non-covalent)

E6E.9: 16 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, W.258, T.259, I.262, M.263, F.266, M.283, S.294, Q.295, F.298 Ligands: EDO.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.266, A:M.283 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., hPDE4D2 structure with inhibitor NPD-425. To be published

Release Date

2019-03-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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