SMTL ID : 6w4c.1

Crystal structure of HAO1 in complex with indazole acid inhibitor - compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315, P.316 Ligands: SL7.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.26, A:Y.27, A:T.80, A:R.315 Hydrogen bonds: A:A.79, A:A.81, A:Q.130, A:Q.130, A:K.236, A:K.236, A:S.258, A:G.261, A:G.292, A:G.293, A:G.314, A:R.315 Water bridges: A:A.79, A:H.260, A:D.291, A:V.294, A:V.294, A:R.315, A:R.315 Salt bridges: A:R.295, A:R.315 FMN.3: 23 residues within 4Å: Chain B: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315, P.316 Ligands: SL7.4 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.26, B:Y.27, B:T.80, B:R.315 Hydrogen bonds: B:A.79, B:A.81, B:Q.130, B:Q.130, B:K.236, B:K.236, B:S.258, B:G.261, B:G.292, B:G.293, B:G.314, B:R.315 Water bridges: B:A.79, B:H.260, B:D.291, B:V.294, B:V.294, B:R.315, B:R.315 Salt bridges: B:R.295, B:R.315 FMN.5: 23 residues within 4Å: Chain C: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315, P.316 Ligands: SL7.6 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:Y.26, C:Y.27, C:T.80, C:R.315 Hydrogen bonds: C:A.79, C:A.81, C:Q.130, C:Q.130, C:K.236, C:K.236, C:S.258, C:G.261, C:G.292, C:G.293, C:G.314, C:R.315 Water bridges: C:A.79, C:H.260, C:D.291, C:V.294, C:V.294, C:R.315, C:R.315 Salt bridges: C:R.295, C:R.315 FMN.7: 23 residues within 4Å: Chain D: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315, P.316 Ligands: SL7.8 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:Y.26, D:Y.27, D:T.80, D:R.315 Hydrogen bonds: D:A.79, D:A.81, D:Q.130, D:Q.130, D:K.236, D:K.236, D:S.258, D:G.261, D:G.292, D:G.293, D:G.314, D:R.315 Water bridges: D:A.79, D:H.260, D:D.291, D:V.294, D:V.294, D:R.315, D:R.315 Salt bridges: D:R.295, D:R.315

4 x SL7: 5-[[3-[3-(dimethylamino)-1,2,4-oxadiazol-5-yl]-2-oxidanyl-phenyl]methylamino]-2~{H}-indazole-3-carboxylic acid(Non-covalent)

SL7.2: 17 residues within 4Å: Chain A: S.22, Y.26, A.81, M.82, M.85, W.110, Y.132, R.167, D.170, R.174, F.175, G.204, A.206, V.209, H.260, R.263 Ligands: FMN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.26, A:A.81, A:W.110, A:Y.132, A:A.206, A:V.209, A:V.209 Hydrogen bonds: A:Y.26, A:Y.26, A:H.260 Water bridges: A:D.170 Salt bridges: A:R.167, A:H.260, A:R.263 SL7.4: 17 residues within 4Å: Chain B: S.22, Y.26, A.81, M.82, M.85, W.110, Y.132, R.167, D.170, R.174, F.175, G.204, A.206, V.209, H.260, R.263 Ligands: FMN.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.26, B:A.81, B:W.110, B:Y.132, B:A.206, B:V.209, B:V.209 Hydrogen bonds: B:Y.26, B:Y.26, B:H.260 Water bridges: B:D.170 Salt bridges: B:R.167, B:H.260, B:R.263 SL7.6: 17 residues within 4Å: Chain C: S.22, Y.26, A.81, M.82, M.85, W.110, Y.132, R.167, D.170, R.174, F.175, G.204, A.206, V.209, H.260, R.263 Ligands: FMN.5 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.26, C:A.81, C:W.110, C:Y.132, C:A.206, C:V.209, C:V.209 Hydrogen bonds: C:Y.26, C:Y.26, C:H.260 Water bridges: C:D.170 Salt bridges: C:R.167, C:H.260, C:R.263 SL7.8: 17 residues within 4Å: Chain D: S.22, Y.26, A.81, M.82, M.85, W.110, Y.132, R.167, D.170, R.174, F.175, G.204, A.206, V.209, H.260, R.263 Ligands: FMN.7 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.26, D:A.81, D:W.110, D:Y.132, D:A.206, D:V.209, D:V.209 Hydrogen bonds: D:Y.26, D:Y.26, D:H.260 Water bridges: D:D.170 Salt bridges: D:R.167, D:H.260, D:R.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, E.C.Y. et al., Discovery of Novel, Potent Inhibitors of Hydroxy Acid Oxidase 1 (HAO1) Using DNA-Encoded Chemical Library Screening. J.Med.Chem. (2021)

Release Date

2021-05-12

Peptides

Hydroxyacid oxidase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Hydroxyacid oxidase 1

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