SMTL ID : 3sl3.4 (3 other biounits)

Crystal structure of the apo form of the catalytic domain of PDE4D2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: D.188, Q.233 Ligands: PEG.11, EDO.27 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: T.70, H.74, E.165 Ligands: EDO.25 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: P.101, D.313 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: V.96, L.97, T.100, W.306, V.310, D.313, A.314, I.317 Ligands: EDO.8 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: L.103, E.104, A.105, V.106, F.107, I.112 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: N.22, K.23, W.24, V.96 Ligands: EDO.5 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: N.22, E.50, R.51, H.95, S.99 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: V.42, H.45, I.65 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: N.224, Y.225, S.226 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: L.163, D.169, F.171, R.179 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: D.78, V.79, A.80, E.260, E.261 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: P.247, L.248, Q.249, T.320 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: E.166, N.167 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: T.56, F.57, K.58, N.173, Q.178 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: T.207, M.208, T.211, D.227 Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain A: Q.49, L.54 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: D.20, K.23, W.24, G.25 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: T.66, T.70, E.165, E.166, C.168 Ligands: EDO.3 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: Y.81, N.243, P.244, T.255, I.258, Q.291 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: D.188, L.191, A.192, K.197, Q.233 Ligands: EDO.1 Ligand excluded by PLIP

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

DMS.2: 3 residues within 4Å: Chain A: S.99, P.101, E.104 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.104 DMS.7: 4 residues within 4Å: Chain A: E.72, D.73, Y.75, N.84 No protein-ligand interaction detected (PLIP)

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

PEG.11: 5 residues within 4Å: Chain A: Q.180, K.184, I.187, D.188 Ligands: EDO.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.180, A:D.188 PEG.13: 6 residues within 4Å: Chain A: T.108, L.110, E.111, S.181, M.185, Y.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.111, A:E.111, A:S.181

2 x ZN: ZINC ION(Non-covalent)

ZN.19: 3 residues within 4Å: Chain A: D.123 Ligands: ZN.20, PO4.21 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.123, H2O.2, H2O.2, H2O.2 ZN.20: 6 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 Ligands: ZN.19, PO4.21 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.21: 6 residues within 4Å: Chain A: H.82, H.86, D.123, D.240 Ligands: ZN.19, ZN.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.240, A:D.240 Water bridges: A:H.82 Salt bridges: A:H.82

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
D

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

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