SMTL ID : 5w49.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 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: L.406, Q.410, K.423, Y.427 Ligands: 9W1.8 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.219, A:D.220, A:V.221, A:I.241, A:D.242, A:N.343, A:N.343, B:Q.410, B:K.423, B:K.423 Water bridges: A:N.188, A:G.222, A:T.239, B:Q.410 NAD.10: 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 Ligands: 9W1.18 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:Q.410, A:Q.410, A:K.423, A:K.423, A:Y.427, B:G.219, B:D.220, B:V.221, B:I.241, B:D.242, B:N.343, B:N.343 Water bridges: B:S.184, B:N.188, B:D.220, B:G.222, B:T.239 NAD.19: 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, K.423, Y.427 Ligands: 9W1.26 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.219, C:D.220, C:V.221, C:T.239, C:I.241, C:D.242, C:N.343, C:N.343, D:K.423, D:K.423, D:Y.427 Water bridges: C:N.188, C:G.222, D:Q.410, D:Q.410 NAD.28: 27 residues within 4Å: Chain C: L.406, Q.410, 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 Ligands: 9W1.36 17 PLIP interactions: 11 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:G.219, D:D.220, D:V.221, D:I.241, D:D.242, D:N.343, D:N.343, C:Q.410, C:Q.410, C:K.423, C:K.423, C:Y.427, C:Y.427 Water bridges: D:S.184, D:N.188, D:N.188, D:G.222

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

EDO.2: 5 residues within 4Å: Chain A: R.202, A.203, K.319, P.320, C.346 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: M.207, A.209, K.211 Chain D: F.353, K.398, L.399 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: L.280, G.281, R.282, D.304, W.307 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: F.353, K.398, L.399 Chain D: M.207, A.209, K.211 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: T.155, V.158, N.176, N.178, D.179 Chain B: H.426 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: N.317, P.320, Q.321, V.322, D.323, E.338 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: A.250, G.253, Y.254, E.255 Chain B: L.399 Chain C: G.210, K.211, V.212, R.235 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: L.280, G.281, R.282, D.304, W.307 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain B: G.210, K.211, V.212, R.235 Chain C: L.399, N.400 Chain D: A.250, Y.254, E.255 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: E.314, V.316, R.324, R.326 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain B: I.21, A.22, E.25, S.352 Chain C: T.204, D.205, V.206 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain B: A.13, W.14, K.17 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: H.426 Chain B: T.155, V.158, H.159, N.178, D.179 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: R.202, A.203, K.319, P.320, C.346 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: R.202, A.203, K.319, P.320, C.346 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: F.353, K.398, L.399 Chain C: M.207, A.209, K.211 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain C: L.280, G.281, R.282, D.304, W.307 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain B: M.207, A.209, K.211 Chain C: F.353, K.398, L.399 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain C: T.155, V.158, N.176, N.178, D.179 Chain D: H.426 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: N.317, P.320, Q.321, V.322, D.323, E.338 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain A: G.210, K.211, V.212, R.235 Chain C: A.250, G.253, Y.254, E.255 Chain D: L.399 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain D: L.280, G.281, R.282, D.304, W.307 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain A: L.399, N.400 Chain B: A.250, Y.254, E.255 Chain D: G.210, K.211, V.212, R.235 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain D: E.314, V.316, R.324, R.326 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: T.204, D.205, V.206 Chain D: I.21, A.22, E.25, S.352 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain D: A.13, W.14, K.17 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain C: H.426 Chain D: T.155, V.158, H.159, N.178, D.179 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain D: R.202, A.203, K.319, P.320, C.346 Ligand excluded by PLIP

4 x 9W1: (4-amino-1,2,5-oxadiazol-3-yl)[(3R)-3-{4-[(3-methoxyphenyl)amino]-6-methylpyridin-2-yl}pyrrolidin-1-yl]methanone(Non-covalent)

9W1.8: 13 residues within 4Å: Chain A: H.52, T.54, E.56, T.57, S.80, Q.82, L.344, A.347, M.348, H.350, M.355, F.359 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.54 Hydrogen bonds: A:T.54, A:E.56, A:T.57, A:H.350 Water bridges: A:F.79 pi-Stacking: A:H.52 9W1.18: 13 residues within 4Å: Chain B: H.52, T.54, E.56, T.57, S.80, Q.82, L.344, A.347, M.348, H.350, M.355, F.359 Ligands: NAD.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.54, B:L.344, B:L.344 Hydrogen bonds: B:T.54, B:E.56, B:E.56, B:T.57, B:H.350 Water bridges: B:F.79 pi-Stacking: B:H.52 9W1.26: 13 residues within 4Å: Chain C: H.52, T.54, E.56, T.57, S.80, Q.82, L.344, A.347, M.348, H.350, M.355, F.359 Ligands: NAD.19 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.54 Hydrogen bonds: C:E.56, C:H.350 Water bridges: C:F.79 pi-Stacking: C:H.52 9W1.36: 13 residues within 4Å: Chain D: H.52, T.54, E.56, T.57, S.80, Q.82, L.344, A.347, M.348, H.350, M.355, F.359 Ligands: NAD.28 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:T.54, D:L.344, D:L.344 Hydrogen bonds: D:E.56, D:H.350 Water bridges: D:F.79 pi-Stacking: D:H.52

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
A

D
B

Adenosylhomocysteinase

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