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

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-3098

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: H.78, E.169 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: S.134, F.266, P.282, C.284 Ligands: E6N.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:P.282 Water bridges: A:Q.269 EDO.5: 3 residues within 4Å: Chain A: K.188, I.191, D.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 EDO.6: 5 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:N.88 Water bridges: A:Y.79 EDO.7: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.199 EDO.8: 6 residues within 4Å: Chain A: T.112, L.114, E.115, S.185, M.189 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.112, A:E.115, A:S.185 EDO.9: 5 residues within 4Å: Chain A: T.60, F.61, K.62, N.177, Q.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.182, A:Q.182 EDO.10: 4 residues within 4Å: Chain A: S.185, K.188, Y.229 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.185 EDO.11: 1 residues within 4Å: Chain A: E.108 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain A: E.54, S.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.103, A:S.103 EDO.16: 4 residues within 4Å: Chain A: D.24, W.28, G.29, H.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.31 EDO.17: 3 residues within 4Å: Chain A: L.147, M.148, N.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.148, A:N.150 Water bridges: A:N.150

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.3 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.3

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

PEG.12: 9 residues within 4Å: Chain A: V.100, L.101, S.103, T.104, W.310, V.314, D.317, A.318 Ligands: PEG.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.103, A:W.310 PEG.13: 3 residues within 4Å: Chain A: P.105, D.317 Ligands: PEG.12 No protein-ligand interaction detected (PLIP)

1 x E6N: (4~{a}~{S},8~{a}~{S})-4-[4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl]-2-[1-(3-nitroimidazo[1,2-b]pyridazin-6-yl)piperidin-4-yl]-4~{a},5,6,7,8,8~{a}-hexahydrophthalazin-1-one(Non-covalent)

E6N.14: 14 residues within 4Å: Chain A: M.199, D.244, L.245, N.247, I.262, M.263, F.266, P.282, M.283, Q.295, G.297, F.298, Y.301 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.266, A:P.282, A:M.283 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298

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

EPE.18: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., hPDE4D2 structure with inhibitor NPD-3098. 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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