SMTL ID : 1y2k.1 (1 other biounit)

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.136, A:D.137, A:D.254, H2O.1, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.137 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1

1 x 7DE: 3,5-DIMETHYL-1-(3-NITROPHENYL)-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER(Non-covalent)

7DE.3: 14 residues within 4Å: Chain A: Y.95, H.96, T.207, M.209, D.254, L.255, N.257, W.268, T.269, I.272, F.276, M.293, Q.305, F.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.257, A:W.268, A:F.308, A:F.308 Hydrogen bonds: A:D.254, A:Q.305 pi-Stacking: A:F.276

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

EDO.4: 3 residues within 4Å: Chain A: K.198, I.201, D.202 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: N.145, Q.146, I.149 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: N.51, E.86, D.87, Y.89, A.91, N.98 Ligands: EDO.8 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: P.115, A.116, S.231, G.232, H.325, P.326, D.327 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99 Ligands: EDO.6 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: L.111, T.114, W.320, V.324, D.327, A.328, I.331 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: A.119, V.120, T.122 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: F.174, F.185, R.193, R.197 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: S.144, N.145, L.165, E.166, D.208, M.209 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: H.168, A.171, V.172, K.175 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: D.92, V.93, P.141, G.142 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: K.303, Q.343, I.346 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: I.149, N.152, S.153, A.156, L.157, D.161 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: H.90, D.139, P.141, L.155 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: R.284, K.296, H.297 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: D.333, E.336, D.337 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: D.270, R.271, E.274 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Card, G.L. et al., A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nat.Biotechnol. (2005)

Release Date

2005-03-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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