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

Crystal Structure of PDE10A with Novel Keto-Benzimidazole Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.87, 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.3 ZN.2: 3 residues within 4Å: Chain A: D.126, E.154 Ligands: ZN.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.126, H2O.1, H2O.1, H2O.3 ZN.11: 6 residues within 4Å: Chain B: H.87, H.91, H.125, D.126, D.236 Ligands: ZN.12 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.6 ZN.12: 3 residues within 4Å: Chain B: D.126, E.154 Ligands: ZN.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, H2O.4, H2O.4, H2O.6 ZN.21: 6 residues within 4Å: Chain C: H.87, H.91, H.125, D.126, D.236 Ligands: ZN.22 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.9 ZN.22: 3 residues within 4Å: Chain C: D.126, E.154 Ligands: ZN.21 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.126, H2O.7, H2O.7, H2O.9

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

SO4.3: 6 residues within 4Å: Chain A: R.82, R.130, H.142 Chain C: F.44, E.45, N.46 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: R.82, R.83 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: K.266, G.269, I.270, Q.271 Chain C: P.245 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: K.69, E.168, G.169, H.170, N.171 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: T.111, D.112 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.80, Q.160, S.163, I.164 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain A: V.84, P.85, R.130, G.131, F.132, E.257, A.260 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain A: F.44, E.45, N.46 Chain B: R.82, R.130, H.142 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.82, R.83 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: P.245 Chain B: K.266, G.269, I.270, Q.271 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: K.69, E.168, G.169, H.170, N.171 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: T.111, D.112 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: N.80, Q.160, S.163, I.164 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain B: V.84, P.85, R.130, G.131, F.132, E.257, A.260 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain B: F.44, E.45, N.46 Chain C: R.82, R.130, H.142 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: R.82, R.83 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: P.245 Chain C: K.266, G.269, I.270, Q.271 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain C: K.69, E.168, G.169, H.170, N.171 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: T.111, D.112 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: N.80, Q.160, S.163, I.164 Ligand excluded by PLIP SO4.29: 7 residues within 4Å: Chain C: V.84, P.85, R.130, G.131, F.132, E.257, A.260 Ligand excluded by PLIP

3 x 2F4: 2-{4-[(6,7-difluoro-1H-benzimidazol-2-yl)amino]phenoxy}-N-methyl-3,4'-bipyridin-2'-amine(Non-covalent)

2F4.10: 17 residues within 4Å: Chain A: Y.86, H.87, L.197, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.86, A:L.237, A:V.240, A:I.254, A:F.258, A:V.284, A:F.291 Hydrogen bonds: A:Y.255, A:G.287, A:Q.288 pi-Stacking: A:F.258, A:F.291, A:F.291 Halogen bonds: A:E.283 2F4.20: 17 residues within 4Å: Chain B: Y.86, H.87, L.197, 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.86, B:L.237, B:V.240, B:I.254, B:F.258, B:V.284, B:F.291 Hydrogen bonds: B:G.287, B:Q.288 pi-Stacking: B:F.258, B:F.291, B:F.291 Halogen bonds: B:E.283 2F4.30: 17 residues within 4Å: Chain C: Y.86, H.87, L.197, 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 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.86, C:L.237, C:V.240, C:I.254, C:F.258, C:V.284, C:F.291 Hydrogen bonds: C:G.287, C:Q.288 pi-Stacking: C:F.258, C:F.291, C:F.291 Halogen bonds: C:E.283

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

Related Entries With Identical Sequence