SMTL ID : 4p0n.2 (1 other biounit)

Crystal structure of PDE10a with a novel Imidazo[4,5-b]pyridine inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-trimer

Ligands

3 x 1IR: N-[cis-3-(2-methoxy-3H-imidazo[4,5-b]pyridin-3-yl)cyclobutyl]-1,3-benzothiazol-2-amine(Non-covalent)

1IR.1: 14 residues within 4Å: Chain A: Y.73, L.224, I.241, Y.242, F.245, P.261, M.262, K.267, E.270, V.271, G.274, Q.275, F.278 Ligands: 1IS.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.224, A:I.241, A:Y.242, A:F.245, A:P.261, A:E.270, A:V.271, A:F.278 Hydrogen bonds: A:Y.242 Water bridges: A:G.274, A:Q.275 pi-Stacking: A:F.278 1IR.10: 14 residues within 4Å: Chain B: Y.73, L.224, I.241, Y.242, F.245, P.261, M.262, K.267, E.270, V.271, G.274, Q.275, F.278 Ligands: 1IS.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.224, B:I.241, B:Y.242, B:F.245, B:P.261, B:E.270, B:V.271, B:F.278 Hydrogen bonds: B:Y.242 Water bridges: B:G.274, B:Q.275 pi-Stacking: B:F.278 1IR.19: 14 residues within 4Å: Chain C: Y.73, L.224, I.241, Y.242, F.245, P.261, M.262, K.267, E.270, V.271, G.274, Q.275, F.278 Ligands: 1IS.20 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.224, C:I.241, C:Y.242, C:F.245, C:P.261, C:E.270, C:V.271, C:F.278 Water bridges: C:G.274, C:Q.275 pi-Stacking: C:F.278

3 x 1IS: N-[trans-3-(2-methoxy-3H-imidazo[4,5-b]pyridin-3-yl)cyclobutyl]-1,3-benzothiazol-2-amine(Non-covalent)

1IS.2: 14 residues within 4Å: Chain A: Y.73, V.227, I.241, Y.242, F.245, P.261, M.262, K.267, E.270, V.271, G.274, Q.275, F.278 Ligands: 1IR.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.241, A:Y.242, A:F.245, A:P.261, A:E.270, A:V.271, A:F.278 Hydrogen bonds: A:Y.242 Water bridges: A:G.274, A:Q.275 pi-Stacking: A:F.278 1IS.11: 14 residues within 4Å: Chain B: Y.73, V.227, I.241, Y.242, F.245, P.261, M.262, K.267, E.270, V.271, G.274, Q.275, F.278 Ligands: 1IR.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.241, B:Y.242, B:F.245, B:P.261, B:E.270, B:V.271, B:F.278 Hydrogen bonds: B:Y.242 Water bridges: B:G.274, B:Q.275 pi-Stacking: B:F.278 1IS.20: 14 residues within 4Å: Chain C: Y.73, V.227, I.241, Y.242, F.245, P.261, M.262, K.267, E.270, V.271, G.274, Q.275, F.278 Ligands: 1IR.19 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.241, C:Y.242, C:F.245, C:P.261, C:E.270, C:V.271, C:F.278 Water bridges: C:G.274, C:Q.275 pi-Stacking: C:F.278

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.78, H.112, D.113, D.223 Ligands: ZN.4 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.78, A:H.112, A:D.113, A:D.223, H2O.2, H2O.6 ZN.4: 2 residues within 4Å: Chain A: D.113 Ligands: ZN.3 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.113, H2O.3, H2O.3, H2O.4, H2O.6, H2O.9 ZN.12: 5 residues within 4Å: Chain B: H.78, H.112, D.113, D.223 Ligands: ZN.13 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.78, B:H.112, B:D.113, B:D.223, H2O.13, H2O.17 ZN.13: 2 residues within 4Å: Chain B: D.113 Ligands: ZN.12 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.113, H2O.13, H2O.14, H2O.15, H2O.17, H2O.20 ZN.21: 5 residues within 4Å: Chain C: H.78, H.112, D.113, D.223 Ligands: ZN.22 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.78, C:H.112, C:D.113, C:D.223, H2O.24, H2O.28 ZN.22: 2 residues within 4Å: Chain C: D.113 Ligands: ZN.21 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.113, H2O.24, H2O.24, H2O.26, H2O.28, H2O.31

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: K.56, L.154, E.155, G.156, H.157, N.158 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.154, A:G.156, A:H.157, A:N.158, A:S.161 Salt bridges: A:K.56 SO4.6: 4 residues within 4Å: Chain A: L.96, L.205, N.206, R.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.96 Salt bridges: A:R.211 SO4.7: 6 residues within 4Å: Chain A: F.31, E.32, N.33 Chain C: R.69, R.117, H.129 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Water bridges: C:R.69 Salt bridges: C:R.69, C:R.117 Hydrogen bonds: A:N.33, A:N.33 SO4.8: 2 residues within 4Å: Chain A: S.164, S.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.165 Water bridges: A:S.166 SO4.14: 6 residues within 4Å: Chain B: K.56, L.154, E.155, G.156, H.157, N.158 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.154, B:G.156, B:H.157, B:N.158, B:S.161 Salt bridges: B:K.56 SO4.15: 4 residues within 4Å: Chain B: L.96, L.205, N.206, R.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.96 Salt bridges: B:R.211 SO4.16: 6 residues within 4Å: Chain A: R.69, R.117, H.129 Chain B: F.31, E.32, N.33 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:R.69 Salt bridges: A:R.69, A:R.117 Hydrogen bonds: B:N.33, B:N.33 SO4.17: 2 residues within 4Å: Chain B: S.164, S.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.165 Water bridges: B:S.166 SO4.23: 6 residues within 4Å: Chain C: K.56, L.154, E.155, G.156, H.157, N.158 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.154, C:G.156, C:H.157, C:N.158, C:S.161 Salt bridges: C:K.56 SO4.24: 4 residues within 4Å: Chain C: L.96, L.205, N.206, R.211 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.96 Salt bridges: C:R.211 SO4.25: 6 residues within 4Å: Chain B: R.69, R.117, H.129 Chain C: F.31, E.32, N.33 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.33, C:N.33 Water bridges: B:R.69 Salt bridges: B:R.69, B:R.117 SO4.26: 2 residues within 4Å: Chain C: S.164, S.165 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.165 Water bridges: C:S.166

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: R.16, E.20, H.25, F.26, D.27 Chain C: K.254, L.255 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.16, A:E.20, A:D.27, A:D.27 Water bridges: A:H.25 GOL.18: 7 residues within 4Å: Chain A: K.254, L.255 Chain B: R.16, E.20, H.25, F.26, D.27 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.16, B:E.20, B:E.20, B:D.27, B:D.27 Water bridges: B:H.25 GOL.27: 7 residues within 4Å: Chain B: K.254, L.255 Chain C: R.16, E.20, H.25, F.26, D.27 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.16, C:E.20, C:E.20, C:D.27, C:D.27 Water bridges: C:H.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, E. et al., Discovery of Novel Imidazo[4,5-b]pyridines as Potent and Selective Inhibitors of Phosphodiesterase 10A (PDE10A). Acs Med.Chem.Lett. (2014)

Release Date

2014-10-01

Peptides

cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A

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