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

Crystal Structure of PDE10A with 1H-benzimidazol-2-yl(4-((3-(tetrahydro-2H-pyran-4-yl)-2-pyridinyl)oxy)phenyl)methanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.91, H.125, D.126, D.236 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.91, A:H.125, A:D.126, A:D.236 ZN.2: 2 residues within 4Å: Chain A: D.126 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.126, H2O.3, H2O.3, H2O.3, H2O.3 ZN.6: 5 residues within 4Å: Chain B: H.91, H.125, D.126, D.236 Ligands: ZN.7 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.91, B:H.125, B:D.126, B:D.236, H2O.4, H2O.6 ZN.7: 3 residues within 4Å: Chain B: D.126, E.154 Ligands: ZN.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.126, H2O.4, H2O.5, H2O.6, H2O.6, H2O.6 ZN.13: 5 residues within 4Å: Chain C: H.91, H.125, D.126, D.236 Ligands: ZN.14 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.91, C:H.125, C:D.126, C:D.236 ZN.14: 2 residues within 4Å: Chain C: D.126 Ligands: ZN.13 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.126, H2O.8, H2O.8, H2O.8, H2O.8 ZN.18: 5 residues within 4Å: Chain D: H.91, H.125, D.126, D.236 Ligands: ZN.19 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.91, D:H.125, D:D.126, D:D.236, H2O.9, H2O.11 ZN.19: 3 residues within 4Å: Chain D: D.126, E.154 Ligands: ZN.18 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.126, H2O.9, H2O.11, H2O.11, H2O.11, H2O.11 ZN.25: 5 residues within 4Å: Chain E: H.91, H.125, D.126, D.236 Ligands: ZN.26 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.91, E:H.125, E:D.126, E:D.236 ZN.26: 2 residues within 4Å: Chain E: D.126 Ligands: ZN.25 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.126, H2O.14, H2O.14, H2O.14, H2O.14 ZN.30: 5 residues within 4Å: Chain F: H.91, H.125, D.126, D.236 Ligands: ZN.31 6 PLIP interactions: 4 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.91, F:H.125, F:D.126, F:D.236, H2O.15, H2O.17 ZN.31: 3 residues within 4Å: Chain F: D.126, E.154 Ligands: ZN.30 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:D.126, H2O.15, H2O.16, H2O.17, H2O.17, H2O.17

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

SO4.3: 5 residues within 4Å: Chain A: K.69, G.169, H.170, N.171, S.174 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: L.109, L.218, N.219, R.224 Chain B: L.109, L.218, N.219, R.224 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain B: K.69, E.168, G.169, H.170, N.171 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain B: R.82, R.83 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain B: S.177, S.178 Chain D: S.177, S.178 Chain F: S.177, S.178 Ligands: SO4.22, SO4.34 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain B: N.171, F.173, S.174, L.176, S.177, Y.181 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain C: K.69, G.169, H.170, N.171, S.174 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain C: L.109, L.218, N.219, R.224 Chain D: L.109, L.218, N.219, R.224 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain D: K.69, E.168, G.169, H.170, N.171 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain D: R.82, R.83 Ligand excluded by PLIP SO4.22: 8 residues within 4Å: Chain B: S.177, S.178 Chain D: S.177, S.178 Chain F: S.177, S.178 Ligands: SO4.10, SO4.34 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain D: N.171, F.173, S.174, L.176, S.177, Y.181 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain E: K.69, G.169, H.170, N.171, S.174 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain E: L.109, L.218, N.219, R.224 Chain F: L.109, L.218, N.219, R.224 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain F: K.69, E.168, G.169, H.170, N.171 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain F: R.82, R.83 Ligand excluded by PLIP SO4.34: 8 residues within 4Å: Chain B: S.177, S.178 Chain D: S.177, S.178 Chain F: S.177, S.178 Ligands: SO4.10, SO4.22 Ligand excluded by PLIP SO4.35: 6 residues within 4Å: Chain F: N.171, F.173, S.174, L.176, S.177, Y.181 Ligand excluded by PLIP

6 x 2W1: 1H-benzimidazol-2-yl(4-{[3-(tetrahydro-2H-pyran-4-yl)pyridin-2-yl]oxy}phenyl)methanone(Non-covalent)

2W1.5: 15 residues within 4Å: Chain A: Y.86, H.87, S.239, V.240, I.254, Y.255, F.258, P.274, M.275, K.280, E.283, V.284, G.287, Q.288, F.291 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.86, A:V.240, A:I.254, A:I.254, A:Y.255, A:F.258, A:P.274, A:E.283, A:V.284, A:F.291 Hydrogen bonds: A:Y.255, A:Y.255, A:Q.288 pi-Stacking: A:F.291 2W1.12: 16 residues within 4Å: Chain B: Y.86, H.87, L.197, S.239, V.240, I.254, Y.255, F.258, P.274, M.275, K.280, E.283, V.284, G.287, Q.288, F.291 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.240, B:I.254, B:Y.255, B:F.258, B:P.274, B:E.283, B:V.284, B:F.291 Hydrogen bonds: B:Y.255, B:Q.288 Water bridges: B:M.275 pi-Stacking: B:F.291 2W1.17: 15 residues within 4Å: Chain C: Y.86, H.87, S.239, V.240, I.254, Y.255, F.258, P.274, M.275, K.280, E.283, V.284, G.287, Q.288, F.291 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.86, C:V.240, C:I.254, C:I.254, C:Y.255, C:F.258, C:P.274, C:E.283, C:V.284, C:F.291 Hydrogen bonds: C:Y.255, C:Y.255, C:Q.288 pi-Stacking: C:F.291 2W1.24: 16 residues within 4Å: Chain D: Y.86, H.87, L.197, S.239, V.240, I.254, Y.255, F.258, P.274, M.275, K.280, E.283, V.284, G.287, Q.288, F.291 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.240, D:I.254, D:Y.255, D:F.258, D:P.274, D:E.283, D:V.284, D:F.291 Hydrogen bonds: D:Y.255, D:Y.255, D:Q.288 Water bridges: D:M.275 pi-Stacking: D:F.291 2W1.29: 15 residues within 4Å: Chain E: Y.86, H.87, S.239, V.240, I.254, Y.255, F.258, P.274, M.275, K.280, E.283, V.284, G.287, Q.288, F.291 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:Y.86, E:V.240, E:I.254, E:I.254, E:Y.255, E:F.258, E:P.274, E:E.283, E:V.284, E:F.291 Hydrogen bonds: E:Y.255, E:Q.288 pi-Stacking: E:F.291 2W1.36: 16 residues within 4Å: Chain F: Y.86, H.87, L.197, S.239, V.240, I.254, Y.255, F.258, P.274, M.275, K.280, E.283, V.284, G.287, Q.288, F.291 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:V.240, F:I.254, F:Y.255, F:F.258, F:P.274, F:E.283, F:V.284, F:F.291 Hydrogen bonds: F:Y.255, F:Y.255, F:Q.288 Water bridges: F:M.275 pi-Stacking: F:F.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, E. et al., Discovery of Clinical Candidate 1-(4-(3-(4-(1H-Benzo[d]imidazole-2-carbonyl)phenoxy)pyrazin-2-yl)piperidin-1-yl)ethanone (AMG 579), A Potent, Selective, and Efficacious Inhibitor of Phosphodiesterase 10A (PDE10A). J.Med.Chem. (2014)

Release Date

2014-08-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

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

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