SMTL ID : 6fe7.3 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-356

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.3: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.1 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: L.114, K.181, Q.182, S.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.181, A:S.185 EDO.7: 6 residues within 4Å: Chain A: N.41, R.42, E.76, D.77, Y.79, N.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:R.42, A:Y.79 EDO.8: 5 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, C.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:S.134 Water bridges: A:S.281 EDO.9: 5 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 Ligands: PG4.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.183 EDO.10: 5 residues within 4Å: Chain A: P.64, D.66, T.67, N.171, Q.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.66, A:T.67, A:Q.176 EDO.11: 6 residues within 4Å: Chain A: L.101, T.104, W.310, D.317, A.318, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.104, A:W.310 EDO.12: 3 residues within 4Å: Chain A: H.80, D.129, P.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.129 EDO.15: 4 residues within 4Å: Chain A: P.251, L.252, D.327, N.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.252 EDO.16: 5 residues within 4Å: Chain A: G.29, H.31, P.251, Q.253 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.29, A:Q.253 EDO.17: 5 residues within 4Å: Chain A: N.26, E.54, R.55, H.99, S.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.26, A:S.103 EDO.18: 3 residues within 4Å: Chain A: M.199, M.203 Ligands: D62.20 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.199, A:M.203 EDO.22: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.41, A:N.88, A:N.88, A:R.261, A:R.261

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 4 residues within 4Å: Chain A: T.74, D.77, H.78, E.169 No protein-ligand interaction detected (PLIP) PG4.21: 8 residues within 4Å: Chain A: Y.149, N.157, L.160, A.161, F.164, R.187, I.191 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.149, A:R.187

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.6 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.6: 3 residues within 4Å: Chain A: D.127, E.156 Ligands: ZN.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.1, H2O.2, H2O.2, H2O.3, H2O.4

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

PEG.13: 7 residues within 4Å: Chain A: D.24, K.27, W.28, G.29, H.31, P.251 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.31 PEG.19: 7 residues within 4Å: Chain A: N.135, Q.136, I.139, S.152, S.153, D.198, S.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.135, A:Q.136, A:S.153, A:S.200 Water bridges: A:Q.136

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

EPE.14: 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 D62: (4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one(Non-covalent)

D62.20: 16 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, T.259, I.262, M.263, F.266, P.282, M.283, Q.295, F.298, I.302 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.298 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-356. To be published

Release Date

2019-04-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

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

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