SMTL ID : 3sl5.3 (3 other biounits)

Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

EPE.1: 8 residues within 4Å: Chain A: H.27, V.28, F.29, R.30, E.33, Q.249, L.250, Q.253 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:F.29, A:R.30, A:R.30, A:Q.249, A:Q.253 Salt bridges: A:H.27, A:E.33, A:E.33

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240, H2O.1 ZN.3: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.3, H2O.4

1 x J25: diethyl 2-[(thiophen-2-ylacetyl)amino]-4,7-dihydrothieno[2,3-c]pyridine-3,6(5H)-dicarboxylate(Non-covalent)

J25.4: 15 residues within 4Å: Chain A: Y.81, M.195, D.240, L.241, N.243, P.244, Y.251, W.254, T.255, I.258, F.262, S.290, Q.291, F.294, I.298 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.241, A:P.244, A:Y.251, A:F.294, A:I.298 Hydrogen bonds: A:Q.291 pi-Stacking: A:F.294

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

EDO.5: 6 residues within 4Å: Chain A: T.56, F.57, K.58, N.173, L.174, Q.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.56, A:Q.178 EDO.6: 3 residues within 4Å: Chain A: L.110, K.177, S.181 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: E.19, V.21, T.46, E.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.19 Water bridges: A:N.22 EDO.8: 5 residues within 4Å: Chain A: D.20, K.23, W.24, G.25, H.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.20, A:W.24 EDO.9: 3 residues within 4Å: Chain A: D.188, K.197, Q.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.188, A:Q.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nankervis, J.L. et al., Thiophene inhibitors of PDE4: Crystal structures show a second binding mode at the catalytic domain of PDE4D2. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-10-26

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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