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

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: D.66, I.69, T.70, M.73 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: S.220, S.221 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: P.105, D.317 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: S.185, K.188, Y.229 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, C.284 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: H.86, H.130, G.132, V.133, S.134, E.265 Ligands: D68.20 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: T.74, H.78, E.169 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.188, I.191, D.192 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: R.55, L.57, D.113, I.116 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: L.102, L.107, E.108, A.109, V.110, F.111, I.116 Ligand excluded by PLIP EDO.16: 1 residues within 4Å: Chain A: E.108 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: T.60, F.61, K.62, N.177, Q.182 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: S.152, N.157 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain A: Q.319 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: T.45, H.49 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: M.199, S.200, H.202, M.203, I.302 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: I.280, S.281, P.282, M.283, C.284, D.285, N.288 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: D.192, L.195, A.196, K.201, Q.237 Ligand excluded by PLIP

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

PG4.2: 3 residues within 4Å: Chain A: L.147, M.148, N.150 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.150

1 x ZN: ZINC ION(Non-covalent)

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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.127, E.156 Ligands: ZN.4 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.5

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

PEG.19: 9 residues within 4Å: Chain A: V.100, L.101, S.103, T.104, W.310, V.314, D.317, A.318, I.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.103, A:T.104, A:W.310

1 x D68: 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione(Non-covalent)

D68.20: 17 residues within 4Å: Chain A: H.86, M.199, D.244, L.245, N.247, P.248, Y.255, W.258, T.259, I.262, F.266, M.283, S.294, Q.295, G.297, F.298 Ligands: EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.245 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298 Halogen bonds: A:S.294

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

EPE.21: 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 NI: NICKEL (II) ION(Non-covalent)

NI.27: 2 residues within 4Å: Chain A: H.80, D.82 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.80, A:D.82, A:D.82, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., hPDE4D2 structure with inhibitor NPD-1439. To be published

Release Date

2019-04-24

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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