SMTL ID : 6w45.1

Crystal structure of HAO1 in complex with biaryl acid inhibitor - compound 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x SLG: 2-chloranyl-4-[2-[[(6-chloranyl-1~{H}-indol-2-yl)carbonyl-methyl-amino]methyl]-5-fluoranyl-phenyl]benzoic acid(Non-covalent)

SLG.1: 16 residues within 4Å: Chain A: S.22, I.23, Y.26, A.81, M.82, M.85, W.110, Y.132, L.164, R.167, L.205, A.206, Y.208, V.209, H.260 Ligands: FMN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.26, A:A.81, A:W.110, A:L.205, A:V.209 Hydrogen bonds: A:R.167 Water bridges: A:H.260 Salt bridges: A:H.260 pi-Stacking: A:Y.26, A:Y.26, A:W.110 SLG.3: 16 residues within 4Å: Chain B: S.22, I.23, Y.26, A.81, M.82, M.85, W.110, Y.132, L.164, R.167, L.205, A.206, Y.208, V.209, H.260 Ligands: FMN.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.26, B:A.81, B:W.110, B:L.205, B:V.209 Hydrogen bonds: B:R.167 Water bridges: B:H.260 Salt bridges: B:H.260 pi-Stacking: B:Y.26, B:Y.26, B:W.110 SLG.5: 16 residues within 4Å: Chain C: S.22, I.23, Y.26, A.81, M.82, M.85, W.110, Y.132, L.164, R.167, L.205, A.206, Y.208, V.209, H.260 Ligands: FMN.6 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.26, C:A.81, C:W.110, C:L.205, C:V.209 Hydrogen bonds: C:R.167 Water bridges: C:H.260 Salt bridges: C:H.260 pi-Stacking: C:Y.26, C:Y.26, C:W.110 SLG.7: 16 residues within 4Å: Chain D: S.22, I.23, Y.26, A.81, M.82, M.85, W.110, Y.132, L.164, R.167, L.205, A.206, Y.208, V.209, H.260 Ligands: FMN.8 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.26, D:A.81, D:W.110, D:L.205, D:V.209 Hydrogen bonds: D:R.167 Water bridges: D:H.260 Salt bridges: D:H.260 pi-Stacking: D:Y.26, D:Y.26, D:W.110

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 22 residues within 4Å: Chain A: Y.27, A.79, T.80, A.81, S.108, W.110, 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 Ligands: SLG.1 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.27, A:R.315 Hydrogen bonds: A:A.79, A:A.81, 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:H.260, A:H.260, A:D.291, A:D.291, A:V.294, A:V.294, A:R.315, A:R.315 Salt bridges: A:R.295, A:R.315 FMN.4: 22 residues within 4Å: Chain B: Y.27, A.79, T.80, A.81, S.108, W.110, 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 Ligands: SLG.3 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.27, B:R.315 Hydrogen bonds: B:A.79, B:A.81, 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:H.260, B:H.260, B:D.291, B:D.291, B:V.294, B:V.294, B:R.315, B:R.315 Salt bridges: B:R.295, B:R.315 FMN.6: 22 residues within 4Å: Chain C: Y.27, A.79, T.80, A.81, S.108, W.110, 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 Ligands: SLG.5 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:Y.27, C:R.315 Hydrogen bonds: C:A.79, C:A.81, 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:H.260, C:H.260, C:D.291, C:D.291, C:V.294, C:V.294, C:R.315, C:R.315 Salt bridges: C:R.295, C:R.315 FMN.8: 22 residues within 4Å: Chain D: Y.27, A.79, T.80, A.81, S.108, W.110, 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 Ligands: SLG.7 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.27, D:R.315 Hydrogen bonds: D:A.79, D:A.81, 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:H.260, D:H.260, D:D.291, D:D.291, D:V.294, D:V.294, D:R.315, D:R.315 Salt bridges: D:R.295, D:R.315

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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