SMTL ID : 6fw3.4 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: D.66, I.69, T.70, M.73 No protein-ligand interaction detected (PLIP) EDO.2: 2 residues within 4Å: Chain A: S.220, S.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.220 Water bridges: A:S.220, A:S.220 EDO.5: 2 residues within 4Å: Chain A: P.105, D.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.317 EDO.6: 3 residues within 4Å: Chain A: S.185, K.188, Y.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.185 Water bridges: A:S.185 EDO.7: 5 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, C.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 Water bridges: A:Q.269 EDO.8: 4 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.183, A:R.187 EDO.10: 1 residues within 4Å: Chain A: E.108 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.108, A:E.108 EDO.11: 3 residues within 4Å: Chain A: T.74, H.78, E.169 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.74, A:E.169 EDO.12: 3 residues within 4Å: Chain A: K.188, I.191, D.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.192 Water bridges: A:K.188 EDO.13: 8 residues within 4Å: Chain A: V.100, L.101, T.104, W.310, V.314, D.317, A.318, I.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.310 EDO.14: 5 residues within 4Å: Chain A: D.24, K.27, W.28, G.29, H.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.28, A:H.31 EDO.15: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.41, A:N.88, A:N.88, A:R.261 Water bridges: A:N.88, A:R.261 EDO.17: 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

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.4 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.6

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.127, E.156 Ligands: ZN.3 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.1, H2O.3, H2O.3, H2O.5, H2O.8

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 7 residues within 4Å: Chain A: N.41, R.42, E.76, D.77, Y.79, H.80, A.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:A.81 Water bridges: A:D.77, A:Y.79

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

EPE.16: 8 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, Q.253, L.254, Q.257 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.31, 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 E8H: 1-(2-{4-[(4aS,8aR)-4-(3,4-dimethoxyphenyl)-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)pyrrolidine-2,5-dione(Non-covalent)

E8H.18: 13 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, T.259, I.262, M.283, S.294, Q.295, G.297, F.298 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.245 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., hPDE4D2 structure with inhibitor NPD-007. 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
D

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

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