SMTL ID : 3gwt.2 (1 other biounit)

Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x 066: 6-{[3-(dimethylcarbamoyl)phenyl]sulfonyl}-4-[(3-methoxyphenyl)amino]-8-methylquinoline-3-carboxamide(Non-covalent)

066.1: 17 residues within 4Å: Chain A: Y.83, H.84, S.132, T.195, M.197, D.242, L.243, N.245, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 Ligands: ARS.7, GOL.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.243, A:I.260, A:F.264, A:F.264 Hydrogen bonds: A:N.245, A:Q.293 Water bridges: A:Y.83, A:Y.83 pi-Stacking: A:F.264, A:F.296, A:F.296 066.11: 17 residues within 4Å: Chain B: Y.83, H.84, S.132, T.195, M.197, D.242, L.243, N.245, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 Ligands: ARS.17, GOL.19 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.243, B:I.260, B:F.264, B:F.264 Hydrogen bonds: B:N.245, B:Q.293 Water bridges: B:Y.83, B:Y.83 pi-Stacking: B:F.264, B:F.296, B:F.296

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.3, ARS.7 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.3, H2O.7 ZN.12: 6 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.13, ARS.17 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.124, B:D.125, B:D.242, H2O.16, H2O.19

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.3, H2O.3, H2O.3, H2O.3, H2O.3 MG.13: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.12 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.15, H2O.15, H2O.16, H2O.16, H2O.16

8 x ARS: ARSENIC(Non-covalent)

ARS.4: 1 residues within 4Å: Chain A: C.44 No protein-ligand interaction detected (PLIP) ARS.5: 2 residues within 4Å: Chain A: E.167, C.170 No protein-ligand interaction detected (PLIP) ARS.6: 3 residues within 4Å: Chain A: S.279, M.281, C.282 No protein-ligand interaction detected (PLIP) ARS.7: 3 residues within 4Å: Chain A: H.84 Ligands: 066.1, ZN.2 No protein-ligand interaction detected (PLIP) ARS.14: 1 residues within 4Å: Chain B: C.44 No protein-ligand interaction detected (PLIP) ARS.15: 2 residues within 4Å: Chain B: E.167, C.170 No protein-ligand interaction detected (PLIP) ARS.16: 3 residues within 4Å: Chain B: S.279, M.281, C.282 No protein-ligand interaction detected (PLIP) ARS.17: 3 residues within 4Å: Chain B: H.84 Ligands: 066.11, ZN.12 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: D.127, E.142, L.143, H.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.156 Water bridges: A:L.143 GOL.9: 6 residues within 4Å: Chain A: M.281, S.292, G.295, F.296, Y.299 Ligands: 066.1 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: T.58, F.59, R.60, N.175, Q.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.59, A:R.60, A:Q.180 GOL.18: 4 residues within 4Å: Chain B: D.127, E.142, L.143, H.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.156 Water bridges: B:L.143 GOL.19: 6 residues within 4Å: Chain B: M.281, S.292, G.295, F.296, Y.299 Ligands: 066.11 No protein-ligand interaction detected (PLIP) GOL.20: 5 residues within 4Å: Chain B: T.58, F.59, R.60, N.175, Q.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.59, B:R.60, B:Q.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woodrow, M.D. et al., Quinolines as a novel structural class of potent and selective PDE4 inhibitors. Optimisation for inhaled administration. Bioorg.Med.Chem.Lett. (2009)

Release Date

2010-04-07

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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