SMTL ID : 7opn.1

Human Aldehyde Oxidase SNP R1231H in complex with Raloxifene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: Q.113, C.114, G.115, C.117, C.149, R.150, C.151, M.753 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.114, A:C.117, A:C.149, A:C.151 FES.2: 10 residues within 4Å: Chain A: G.43, C.44, G.45, G.47, G.48, C.49, G.50, C.52, N.72, C.74 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.49, A:C.52, A:C.74 FES.12: 9 residues within 4Å: Chain B: Q.113, C.114, G.115, C.117, C.149, R.150, C.151, T.152, M.753 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.114, B:C.117, B:C.149, B:C.151 FES.13: 10 residues within 4Å: Chain B: G.43, C.44, G.45, G.47, G.48, C.49, G.50, C.52, N.72, C.74 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.49, B:C.52, B:C.74

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.3: 20 residues within 4Å: Chain A: Q.113, C.151, G.805, A.806, F.807, G.808, R.921, M.1047, G.1048, Q.1049, G.1087, G.1088, S.1089, V.1090, V.1091, A.1092, Q.1203, G.1269, E.1270 Ligands: MOS.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.113, A:A.806, A:F.807, A:M.1047, A:Q.1049, A:V.1091, A:A.1092, A:Q.1203, A:Q.1203, A:G.1269 MTE.14: 20 residues within 4Å: Chain B: Q.113, C.151, G.805, A.806, F.807, G.808, R.921, M.1047, G.1048, Q.1049, G.1087, G.1088, S.1089, V.1090, V.1091, A.1092, Q.1203, G.1269, E.1270 Ligands: MOS.15 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.113, B:A.806, B:F.807, B:M.1047, B:Q.1049, B:V.1091, B:A.1092, B:Q.1203, B:Q.1203, B:G.1269 Water bridges: B:R.921

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

MOS.4: 10 residues within 4Å: Chain A: Q.776, G.808, A.919, F.920, R.921, S.1086, G.1087, G.1088, E.1270 Ligands: MTE.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.776, A:G.1088 MOS.15: 10 residues within 4Å: Chain B: Q.776, G.808, A.919, F.920, R.921, S.1086, G.1087, G.1088, E.1270 Ligands: MTE.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.776, B:G.1088

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

FAD.5: 27 residues within 4Å: Chain A: G.46, G.47, P.263, V.264, I.265, M.266, G.267, N.268, T.269, S.270, V.271, L.312, L.344, A.345, I.349, A.353, S.354, G.357, H.358, I.360, H.363, D.365, S.366, D.367, I.410, L.411, L.438 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.345, A:I.349 Hydrogen bonds: A:V.264, A:M.266, A:G.267, A:N.268, A:T.269, A:S.270, A:V.271, A:A.345, A:S.354, A:H.358, A:D.367, A:D.367, A:L.411, A:L.411 Water bridges: A:R.429, A:A.439 FAD.16: 26 residues within 4Å: Chain B: G.46, G.47, P.263, V.264, I.265, M.266, G.267, N.268, T.269, S.270, V.271, L.344, A.345, I.349, A.353, S.354, G.357, H.358, I.360, H.363, D.365, S.366, D.367, I.410, L.411, L.438 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.345, B:I.349 Hydrogen bonds: B:V.264, B:M.266, B:G.267, B:N.268, B:T.269, B:T.269, B:S.270, B:V.271, B:A.345, B:S.354, B:H.358, B:D.367, B:D.367, B:D.367, B:L.411, B:L.411 Water bridges: B:D.365

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.6: 7 residues within 4Å: Chain A: I.56, R.58, H.69, A.71, S.80, L.81, M.352 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.58, A:H.69 MLI.18: 7 residues within 4Å: Chain B: E.740, K.854, Y.855, K.856, D.869, M.870, E.871 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.854 Hydrogen bonds: B:E.740, B:K.854, B:K.856

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.7: 16 residues within 4Å: Chain A: H.799, V.800, R.801, R.1073, G.1074, T.1075, S.1076, E.1078 Chain B: H.799, V.800, R.801, R.1073, G.1074, T.1075, S.1076, E.1078 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:S.1076, B:H.799, B:V.800, B:T.1075, B:S.1076

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: P.23, M.241, N.268, V.271, V.275 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.268, A:N.268 GOL.9: 7 residues within 4Å: Chain A: E.740, K.854, Y.855, K.856, D.869, M.870, E.871 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.740, A:K.854, A:K.856, A:D.869 GOL.17: 8 residues within 4Å: Chain B: C.44, G.48, L.148, R.433, F.751, Y.1236, K.1237, I.1238 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.48, B:R.433, B:R.433, B:Y.1236, B:K.1237, B:I.1238

4 x RAL: RALOXIFENE(Non-covalent)

RAL.10: 10 residues within 4Å: Chain A: F.653, F.655, F.656, F.777, Y.780, D.783, V.811, L.812, E.882 Chain B: Q.1127 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.653, A:F.656, A:F.656, A:F.777, A:Y.780, A:V.811 Hydrogen bonds: A:D.783 pi-Stacking: A:F.656, A:F.777 RAL.11: 9 residues within 4Å: Chain A: E.451, G.452, D.453, G.454, H.484, N.486, D.538, H.541, Y.542 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.484, A:Y.542 Hydrogen bonds: A:G.452, A:G.454, A:N.486 pi-Stacking: A:H.541 RAL.20: 9 residues within 4Å: Chain A: Q.1127 Chain B: F.653, F.655, F.656, F.777, Y.780, D.783, V.811, E.882 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.653, B:F.656, B:F.656, B:F.777, B:Y.780, B:V.811 pi-Stacking: B:F.656, B:F.777 RAL.21: 9 residues within 4Å: Chain B: E.451, G.452, D.453, G.454, H.484, N.486, D.538, H.541, Y.542 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.542 Hydrogen bonds: B:G.452, B:N.486 pi-Stacking: B:H.541, B:H.541

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.19: 6 residues within 4Å: Chain B: R.58, H.69, I.76, S.80, L.81, M.352 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mota, C. et al., Interrogating the Inhibition Mechanisms of Human Aldehyde Oxidase by X-ray Crystallography and NMR Spectroscopy: The Raloxifene Case. J.Med.Chem. (2021)

Release Date

2021-09-01

Peptides

Aldehyde oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aldehyde oxidase