SMTL ID : 5w4b.1 (1 other biounit)

The crystal structure of human S-adenosylhomocysteine hydrolase (AHCY) bound to benzothiazole inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: D.187, N.188, C.192, G.217, G.219, D.220, V.221, T.239, E.240, I.241, D.242, N.245, T.272, T.273, G.274, C.275, I.278, I.296, G.297, H.298, L.341, N.343, H.350 Chain B: Q.410, L.414, K.423, Y.427 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.188, A:D.220, A:V.221, A:I.241, A:D.242, A:H.298, A:N.343, A:N.343, B:Q.410, B:K.423, B:K.423 Water bridges: A:T.155, A:G.219, A:G.222, A:T.239, B:Q.410 NAD.3: 27 residues within 4Å: Chain A: L.406, Q.410, K.423, Y.427 Chain B: D.187, N.188, C.192, G.217, G.219, D.220, V.221, T.239, E.240, I.241, D.242, N.245, T.272, T.273, G.274, C.275, I.278, I.296, G.297, H.298, L.341, N.343, H.350 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.220, B:V.221, B:I.241, B:D.242, B:I.296, B:N.343, A:Q.410, A:Q.410, A:K.423, A:K.423, A:Y.427 Water bridges: B:T.155, B:N.188, B:G.219, B:G.222, B:T.239, B:H.298, B:H.298, B:H.298 NAD.5: 28 residues within 4Å: Chain C: D.187, N.188, C.192, G.217, G.219, D.220, V.221, T.239, E.240, I.241, D.242, N.245, T.272, T.273, G.274, C.275, I.278, I.296, G.297, H.298, L.341, N.343, H.350 Chain D: L.406, Q.410, L.414, K.423, Y.427 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:D.220, C:V.221, C:I.241, C:D.242, C:N.343, C:N.343, D:Q.410, D:Q.410, D:K.423, D:K.423, D:Y.427, D:Y.427 Water bridges: C:N.188, C:G.219, C:G.222, C:H.298 NAD.8: 28 residues within 4Å: Chain C: L.406, Q.410, L.414, K.423, Y.427 Chain D: D.187, N.188, C.192, G.217, G.219, D.220, V.221, T.239, E.240, I.241, D.242, N.245, T.272, T.273, G.274, C.275, I.278, I.296, G.297, H.298, L.341, N.343, H.350 16 PLIP interactions: 10 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:N.188, D:D.220, D:V.221, D:I.241, D:D.242, D:N.343, D:N.343, C:Q.410, C:K.423, C:K.423, C:Y.427, C:Y.427 Water bridges: D:G.219, D:G.222, D:F.299, C:Q.410

4 x 9W4: 4-[(2,5-dioxo-2,5-dihydro-1H-imidazol-1-yl)methyl]-N-[2-(morpholin-4-yl)-1,3-benzothiazol-6-yl]benzamide(Non-covalent)

9W4.2: 12 residues within 4Å: Chain A: H.52, T.54, E.56, N.77, F.79, S.80, Q.321, R.340, L.344, G.349, H.350, M.355 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.79, A:L.344, A:L.344 Hydrogen bonds: A:T.54, A:E.56, A:H.350 pi-Stacking: A:H.52 9W4.4: 12 residues within 4Å: Chain B: H.52, T.54, E.56, N.77, F.79, S.80, R.340, L.344, M.348, G.349, H.350, M.355 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.344, B:L.344 Hydrogen bonds: B:T.54, B:E.56, B:H.350 pi-Stacking: B:H.52 9W4.6: 13 residues within 4Å: Chain C: H.52, T.54, E.56, N.77, F.79, S.80, Q.321, R.340, L.344, G.349, H.350, M.355 Ligands: EDO.7 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.79, C:L.344, C:L.344 Hydrogen bonds: C:Q.321, C:H.350 pi-Stacking: C:H.52 9W4.9: 13 residues within 4Å: Chain D: H.52, T.54, E.56, N.77, F.79, S.80, Q.321, R.340, L.344, M.348, G.349, H.350, M.355 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.79, D:L.344, D:L.344 Hydrogen bonds: D:Q.321, D:H.350 pi-Stacking: D:H.52

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain C: R.340, L.341, G.345 Ligands: 9W4.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.341 Water bridges: C:R.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uchiyama, N. et al., Identification of AHCY inhibitors using novel high-throughput mass spectrometry. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-06-28

Peptides

Adenosylhomocysteinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

Adenosylhomocysteinase

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