SMTL ID : 4mvh.3 (2 other biounits)

Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

6 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.91, A:H.125, A:D.126, A:D.236, H2O.1 ZN.2: 2 residues within 4Å: Chain A: D.126 Ligands: ZN.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, H2O.2 ZN.9: 5 residues within 4Å: Chain B: H.91, H.125, D.126, D.236 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.91, B:H.125, B:D.126, B:D.236, H2O.3 ZN.10: 2 residues within 4Å: Chain B: D.126 Ligands: ZN.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, H2O.4 ZN.17: 5 residues within 4Å: Chain C: H.91, H.125, D.126, D.236 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.91, C:H.125, C:D.126, C:D.236, H2O.5 ZN.18: 2 residues within 4Å: Chain C: D.126 Ligands: ZN.17 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.126, H2O.6

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

SO4.3: 7 residues within 4Å: Chain A: R.82, R.130, H.142 Chain B: F.44, E.45, N.46, M.47 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.45, B:N.46, B:N.46, B:M.47 Salt bridges: A:R.82, A:R.130, A:H.142 SO4.4: 3 residues within 4Å: Chain A: Y.81, R.82, R.83 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.83 SO4.5: 5 residues within 4Å: Chain A: K.69, E.168, G.169, H.170, N.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.169, A:N.171 Salt bridges: A:K.69 SO4.6: 2 residues within 4Å: Chain A: T.111, D.112 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.112 SO4.7: 5 residues within 4Å: Chain A: N.80, Q.160, S.163, I.164, L.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.80, A:Q.160, A:S.163 Water bridges: A:S.76 SO4.11: 7 residues within 4Å: Chain B: R.82, R.130, H.142 Chain C: F.44, E.45, N.46, M.47 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:E.45, C:N.46, C:N.46, C:M.47 Salt bridges: B:R.82, B:R.130, B:H.142 SO4.12: 3 residues within 4Å: Chain B: Y.81, R.82, R.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.83 SO4.13: 5 residues within 4Å: Chain B: K.69, E.168, G.169, H.170, N.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.169, B:N.171 Salt bridges: B:K.69 SO4.14: 2 residues within 4Å: Chain B: T.111, D.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.112 SO4.15: 5 residues within 4Å: Chain B: N.80, Q.160, S.163, I.164, L.167 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.80, B:Q.160, B:S.163 Water bridges: B:S.76 SO4.19: 7 residues within 4Å: Chain A: F.44, E.45, N.46, M.47 Chain C: R.82, R.130, H.142 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Salt bridges: C:R.82, C:R.130, C:H.142 Hydrogen bonds: A:E.45, A:N.46, A:N.46, A:M.47 SO4.20: 3 residues within 4Å: Chain C: Y.81, R.82, R.83 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.83 SO4.21: 5 residues within 4Å: Chain C: K.69, E.168, G.169, H.170, N.171 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.169, C:N.171 Salt bridges: C:K.69 SO4.22: 2 residues within 4Å: Chain C: T.111, D.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.112 SO4.23: 5 residues within 4Å: Chain C: N.80, Q.160, S.163, I.164, L.167 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.80, C:Q.160, C:S.163 Water bridges: C:S.76

3 x 2F5: 1H-BENZIMIDAZOL-2-YL(4-{[3-(MORPHOLIN-4-YL)PYRAZIN-2-YL]OXY}PHENYL)METHANONE(Non-covalent)

2F5.8: 16 residues within 4Å: Chain A: Y.86, H.87, L.237, 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.258, A:P.274, A:E.283, A:V.284, A:F.291 Hydrogen bonds: A:Y.255, A:Q.288 Water bridges: A:M.275 pi-Stacking: A:F.291, A:F.291 2F5.16: 16 residues within 4Å: Chain B: Y.86, H.87, L.237, 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 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: 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, B:F.291 2F5.24: 16 residues within 4Å: Chain C: Y.86, H.87, L.237, 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.258, C:P.274, C:E.283, C:V.284, C:F.291 Hydrogen bonds: C:Q.288 Water bridges: C:M.275 pi-Stacking: C:F.291, C:F.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, E. et al., Design, Optimization, and Biological Evaluation of Novel Keto-Benzimidazoles as Potent and Selective Inhibitors of Phosphodiesterase 10A (PDE10A). J.Med.Chem. (2013)

Release Date

2013-10-23

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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