SMTL ID : 4p1r.1 (1 other biounit)

Crystal Structure of PDE10A with Imidazo[4,5-b]pyridines as Potent and Selective Inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.74, H.78, H.112, D.113, D.223 Ligands: ZN.2 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.7, H2O.10 ZN.2: 3 residues within 4Å: Chain A: H.112, D.113 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.113, H2O.4, H2O.5, H2O.5, H2O.7, H2O.7 ZN.21: 6 residues within 4Å: Chain B: H.74, H.78, H.112, D.113, D.223 Ligands: ZN.22 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.20, H2O.24 ZN.22: 3 residues within 4Å: Chain B: H.112, D.113 Ligands: ZN.21 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.113, H2O.18, H2O.19, H2O.19, H2O.20, H2O.20 ZN.41: 6 residues within 4Å: Chain C: H.74, H.78, H.112, D.113, D.223 Ligands: ZN.42 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.34, H2O.37 ZN.42: 3 residues within 4Å: Chain C: H.112, D.113 Ligands: ZN.41 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.113, H2O.31, H2O.32, H2O.32, H2O.34, H2O.34

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

SO4.3: 6 residues within 4Å: Chain A: F.31, E.32, N.33, M.34 Chain B: R.69, R.117 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: K.56, E.155, G.156, H.157, N.158 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain A: V.71, P.72, R.117, G.118, F.119, E.244, A.247 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: L.96, L.205, N.206, R.211 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: R.69, R.70 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: L.184, F.188, F.278, V.282 Ligands: GOL.18, 2KR.20 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: Q.91, N.92 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: L.134, Y.135, S.136, T.137, Q.142 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: N.67, Q.147, S.150, I.151 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: N.158, F.160, S.161, L.163, S.164, Y.168 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: F.97, T.98, D.99, R.102 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: R.45, Q.91, H.94 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain B: F.31, E.32, N.33, M.34 Chain C: R.69, R.117 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain B: K.56, E.155, G.156, H.157, N.158 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain B: V.71, P.72, R.117, G.118, F.119, E.244, A.247 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain B: L.96, L.205, N.206, R.211 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain B: R.69, R.70 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain B: L.184, F.188, F.278, V.282 Ligands: GOL.38, 2KR.40 Ligand excluded by PLIP SO4.29: 2 residues within 4Å: Chain B: Q.91, N.92 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain B: L.134, Y.135, S.136, T.137, Q.142 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain B: N.67, Q.147, S.150, I.151 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain B: N.158, F.160, S.161, L.163, S.164, Y.168 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain B: F.97, T.98, D.99, R.102 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: R.45, Q.91, H.94 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain A: R.69, R.117 Chain C: F.31, E.32, N.33, M.34 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain C: K.56, E.155, G.156, H.157, N.158 Ligand excluded by PLIP SO4.45: 7 residues within 4Å: Chain C: V.71, P.72, R.117, G.118, F.119, E.244, A.247 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain C: L.96, L.205, N.206, R.211 Ligand excluded by PLIP SO4.47: 2 residues within 4Å: Chain C: R.69, R.70 Ligand excluded by PLIP SO4.48: 6 residues within 4Å: Chain C: L.184, F.188, F.278, V.282 Ligands: GOL.58, 2KR.60 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain C: Q.91, N.92 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain C: L.134, Y.135, S.136, T.137, Q.142 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain C: N.67, Q.147, S.150, I.151 Ligand excluded by PLIP SO4.52: 6 residues within 4Å: Chain C: N.158, F.160, S.161, L.163, S.164, Y.168 Ligand excluded by PLIP SO4.53: 4 residues within 4Å: Chain C: F.97, T.98, D.99, R.102 Ligand excluded by PLIP SO4.59: 3 residues within 4Å: Chain C: R.45, Q.91, H.94 Ligand excluded by PLIP

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: S.209, H.210, R.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.209, A:S.209, A:R.213 GOL.15: 8 residues within 4Å: Chain A: R.16, E.20, H.25, F.26, D.27, L.230 Chain B: K.254, L.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.16, A:D.27, A:D.27 GOL.16: 5 residues within 4Å: Chain A: W.231, P.232, K.235, L.236 Chain B: K.253 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.253 GOL.17: 5 residues within 4Å: Chain A: P.232 Chain B: K.253, G.256, I.257, Q.258 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.258 GOL.18: 5 residues within 4Å: Chain A: I.260, P.261, M.262 Ligands: SO4.8, 2KR.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.262 GOL.34: 3 residues within 4Å: Chain B: S.209, H.210, R.213 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.209, B:S.209, B:R.213 GOL.35: 8 residues within 4Å: Chain B: R.16, E.20, H.25, F.26, D.27, L.230 Chain C: K.254, L.255 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.16, B:D.27, B:D.27 GOL.36: 5 residues within 4Å: Chain B: W.231, P.232, K.235, L.236 Chain C: K.253 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.253 GOL.37: 5 residues within 4Å: Chain B: P.232 Chain C: K.253, G.256, I.257, Q.258 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.258 GOL.38: 5 residues within 4Å: Chain B: I.260, P.261, M.262 Ligands: SO4.28, 2KR.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.262 GOL.54: 3 residues within 4Å: Chain C: S.209, H.210, R.213 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.209, C:S.209, C:R.213 GOL.55: 8 residues within 4Å: Chain A: K.254, L.255 Chain C: R.16, E.20, H.25, F.26, D.27, L.230 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.16, C:D.27, C:D.27 GOL.56: 5 residues within 4Å: Chain A: K.253 Chain C: W.231, P.232, K.235, L.236 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.253 GOL.57: 5 residues within 4Å: Chain A: K.253, G.256, I.257, Q.258 Chain C: P.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.258 GOL.58: 5 residues within 4Å: Chain C: I.260, P.261, M.262 Ligands: SO4.48, 2KR.60 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.262

3 x 2KR: N-[4-(2-methoxy-3H-imidazo[4,5-b]pyridin-3-yl)phenyl]-5-methylpyridin-2-amine(Non-covalent)

2KR.20: 16 residues within 4Å: Chain A: L.184, S.226, 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: SO4.8, GOL.18 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.227, A:I.241, A:Y.242, A:F.245, A:P.261, A:M.262, A:K.267, A:E.270, A:F.278, A:F.278 Hydrogen bonds: A:Q.275 Water bridges: A:G.274 pi-Stacking: A:F.278 2KR.40: 16 residues within 4Å: Chain B: L.184, S.226, 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: SO4.28, GOL.38 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.227, B:I.241, B:Y.242, B:F.245, B:P.261, B:M.262, B:K.267, B:E.270, B:F.278, B:F.278 Hydrogen bonds: B:Q.275 Water bridges: B:G.274 pi-Stacking: B:F.278 2KR.60: 16 residues within 4Å: Chain C: L.184, S.226, 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: SO4.48, GOL.58 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.227, C:I.241, C:Y.242, C:F.245, C:P.261, C:M.262, C:K.267, C:E.270, C:F.278, C:F.278 Hydrogen bonds: C:Y.242, C:Q.275 Water bridges: C:G.274 pi-Stacking: C:F.278

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

2014-07-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

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

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