SMTL ID : 6hwo.2 (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

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

EDO.1: 3 residues within 4Å: Chain A: Q.136, I.139 Ligands: DMS.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.136 EDO.2: 5 residues within 4Å: Chain A: D.260, M.263, E.264, F.267, V.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.260, A:E.264 EDO.3: 4 residues within 4Å: Chain A: A.109, V.110, F.111, T.112 No protein-ligand interaction detected (PLIP) EDO.4: 7 residues within 4Å: Chain A: M.212, T.215, K.216, K.217, L.224, L.225, L.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.215, A:T.215, A:K.217, A:K.217 EDO.5: 4 residues within 4Å: Chain A: N.41, A.81, N.88, I.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41, A:N.41 EDO.6: 6 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, D.317, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.310, A:D.317 EDO.7: 4 residues within 4Å: Chain A: I.299, D.300, H.304, R.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.300, A:H.304 EDO.9: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.144, A:E.144 EDO.14: 3 residues within 4Å: Chain A: K.188, I.191, D.192 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.144

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.13 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.4

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

DMS.10: 3 residues within 4Å: Chain A: N.135, Q.136 Ligands: EDO.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.135, A:Q.136, A:S.200

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

PEG.11: 3 residues within 4Å: Chain A: T.74, H.78, E.169 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.169

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.12: 14 residues within 4Å: Chain A: H.86, M.199, D.244, L.245, N.247, T.259, I.262, M.263, M.283, V.291, S.294, Q.295, G.297, F.298 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.245, 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.13: 2 residues within 4Å: Chain A: D.127 Ligands: ZN.8 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.4

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

EPE.16: 7 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, L.254, Q.257 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.257 Salt bridges: A:H.31, A:E.37, A:E.37

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
B

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

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