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

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: E.108 Ligands: DMS.2 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: T.74, H.78, E.169 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: P.105, D.317 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: V.100, L.101, T.104, W.310, V.314, D.317, A.318, I.321 Ligands: EDO.8 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: L.107, E.108, A.109, V.110, F.111, I.116 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: N.26, K.27, W.28, V.100 Ligands: EDO.5 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: H.49 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: D.82, V.83, A.84, E.265, R.268 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: T.60, F.61, K.62, N.177, T.179, Q.182 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: D.24, K.27, W.28, G.29 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: D.192, L.195, A.196, Q.237 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: L.147, M.148, N.150 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: I.69, T.70 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: F.164, L.167, F.175, R.183, R.187 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: M.212, T.215, K.216, K.217, L.224, L.225 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: T.112, E.115, S.185, M.189, Y.229 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: A.109, V.110, F.111 Ligand excluded by PLIP

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: S.103, T.104, P.105, E.108 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.108 DMS.7: 4 residues within 4Å: Chain A: E.76, D.77, Y.79, N.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.81

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.16 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.2, H2O.5

1 x FFZ: 3-[5-[(4aR,8aS)-4-OXIDANYLIDENE-3-PROPAN-2-YL-4a,5,8,8a-TETRAHYDROPHTHALAZIN-1-YL]-2-METHOXY-PHENYL]-N-(PHENYLMETHYL)PROP-2-YNAMIDE

FFZ.15: 11 residues within 4Å: Chain A: H.86, M.199, D.244, L.245, N.247, I.262, M.283, S.294, Q.295, G.297, F.298 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.245, A:F.298, A:F.298, A:F.298 Hydrogen bonds: A:S.294, A:Q.295 pi-Stacking: A:F.298

1 x MG: MAGNESIUM ION(Non-covalent)

MG.16: 3 residues within 4Å: Chain A: D.127, E.156 Ligands: ZN.12 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.2, H2O.2, H2O.3, H2O.4, H2O.4

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

EPE.23: 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.24: 5 residues within 4Å: Chain A: L.58, K.62, I.63, P.64, V.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.62, A:V.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Heuvel, E. et al., Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2). Bioorg.Med.Chem. (2019)

Release Date

2019-07-24

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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