SMTL ID : 3am9.1

Complex of bovine xanthine dehydrogenase and trihydroxy FYX-051

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 8 residues within 4Å: Chain A: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.744 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.113, A:C.116, A:C.148, A:C.150 FES.2: 10 residues within 4Å: Chain A: G.42, C.43, G.44, G.46, G.47, C.48, G.49, C.51, N.71, C.73 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.43, A:C.48, A:C.51, A:C.73 FES.10: 8 residues within 4Å: Chain B: Q.112, C.113, G.114, C.116, C.148, R.149, C.150, L.744 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.113, B:C.116, B:C.148, B:C.150 FES.11: 10 residues within 4Å: Chain B: G.42, C.43, G.44, G.46, G.47, C.48, G.49, C.51, N.71, C.73 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.43, B:C.48, B:C.51, B:C.73

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: A.867, S.870, R.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.867, A:S.870, A:S.874, A:S.907, A:N.908 CA.9: 5 residues within 4Å: Chain A: H.741, Y.743, D.832, T.836, G.837 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.741, A:Y.743, A:T.836, A:G.837, H2O.38 CA.12: 7 residues within 4Å: Chain B: A.867, S.870, R.871, D.872, S.874, S.907, N.908 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:A.867, B:S.870, B:S.874, B:S.907, B:N.908 CA.19: 5 residues within 4Å: Chain B: H.741, Y.743, D.832, T.836, G.837 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.741, B:Y.743, B:T.836, B:G.837, H2O.73

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.4: 32 residues within 4Å: Chain A: E.45, G.46, G.47, L.74, K.256, L.257, V.258, V.259, G.260, N.261, T.262, E.263, I.264, L.287, A.301, W.336, F.337, A.338, V.342, A.346, S.347, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:L.74, A:A.338, A:V.342 Hydrogen bonds: A:L.257, A:L.257, A:V.259, A:G.260, A:N.261, A:T.262, A:T.262, A:E.263, A:I.264, A:A.338, A:S.347, A:N.351, A:T.354, A:T.354, A:D.360, A:D.360, A:D.360, A:L.404, A:L.404, A:K.422 Water bridges: A:K.256, A:K.256, A:S.347, A:A.432 pi-Stacking: A:F.337 FAD.13: 30 residues within 4Å: Chain B: E.45, G.46, G.47, L.74, K.256, L.257, V.258, V.259, G.260, N.261, T.262, E.263, I.264, A.301, F.337, A.338, V.342, A.346, S.347, G.350, N.351, I.353, T.354, S.359, D.360, I.403, L.404, K.422, D.429, D.430 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.74, B:A.338, B:V.342 Hydrogen bonds: B:L.257, B:L.257, B:V.259, B:G.260, B:N.261, B:T.262, B:E.263, B:I.264, B:A.338, B:V.345, B:S.347, B:N.351, B:T.354, B:T.354, B:D.360, B:D.360, B:L.404, B:L.404, B:K.422 Water bridges: B:S.347 pi-Stacking: B:F.337

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.5: 9 residues within 4Å: Chain A: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.840, A:F.911, A:F.911 BCT.14: 9 residues within 4Å: Chain B: R.839, H.840, I.877, T.909, A.910, F.911, F.914, G.915, Q.918 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.839, B:F.911, B:F.914, B:G.915, B:Q.918

2 x MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER(Non-covalent)

MTE.6: 20 residues within 4Å: Chain A: Q.112, C.150, G.796, G.797, F.798, G.799, R.912, M.1038, G.1039, Q.1040, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 Ligands: MOS.7, FYO.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.112, A:G.797, A:F.798, A:R.912, A:M.1038, A:Q.1040, A:S.1082, A:S.1082, A:T.1083, A:Q.1194, A:Q.1194 Water bridges: A:R.912 MTE.15: 20 residues within 4Å: Chain B: Q.112, C.150, G.796, G.797, F.798, G.799, R.912, M.1038, G.1039, Q.1040, A.1078, A.1079, S.1080, V.1081, S.1082, Q.1194, G.1260, E.1261 Ligands: MOS.16, FYO.17 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.112, B:G.797, B:F.798, B:M.1038, B:Q.1040, B:S.1082, B:S.1082, B:S.1082, B:Q.1194, B:Q.1194, B:G.1260 Water bridges: B:Q.112, B:R.912

2 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)

MOS.7: 11 residues within 4Å: Chain A: Q.767, F.798, G.799, E.802, A.910, F.911, R.912, A.1078, E.1261 Ligands: MTE.6, FYO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.767 MOS.16: 11 residues within 4Å: Chain B: Q.767, G.799, E.802, A.910, F.911, R.912, T.1077, A.1078, E.1261 Ligands: MTE.15, FYO.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.767, B:E.802

2 x FYO: 4-[5-(2,6-dioxo-1,2,3,6-tetrahydropyridin-4-yl)-1H-1,2,4-triazol-3-yl]-6-oxo-1,6-dihydropyridine-2-carbonitrile(Non-covalent)

FYO.8: 15 residues within 4Å: Chain A: L.648, E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, F.1013, L.1014, A.1078, A.1079, E.1261 Ligands: MTE.6, MOS.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.648, A:L.873, A:F.1009, A:L.1014 Hydrogen bonds: A:S.876, A:R.880, A:R.880, A:A.1079 pi-Stacking: A:F.914 FYO.17: 16 residues within 4Å: Chain B: L.648, K.771, E.802, L.873, S.876, R.880, F.914, S.1008, F.1009, V.1011, L.1014, A.1078, A.1079, E.1261 Ligands: MTE.15, MOS.16 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.873, B:V.1011, B:L.1014 Hydrogen bonds: B:R.880, B:A.1079 Water bridges: B:S.876 pi-Stacking: B:F.914, B:F.1009

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 9 residues within 4Å: Chain B: C.662, G.664, H.665, I.666, R.804, I.835, N.869, S.906, S.907 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.664, B:H.665, B:I.666, B:N.869, B:S.906, B:S.907 Water bridges: B:R.804, B:R.804 GOL.20: 6 residues within 4Å: Chain B: D.594, F.604, P.675, R.824, C.825, M.826 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.826 Water bridges: B:M.826, B:D.828

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, K. et al., FYX-051: A Novel and Potent Hybrid-Type Inhibitor of Xanthine Oxidoreductase. J.Pharmacol.Exp.Ther. (2011)

Release Date

2010-11-03

Peptides

Xanthine dehydrogenase/oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xanthine dehydrogenase/oxidase

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