SMTL ID : 7m2o.1

Crystal structure of Human Glycolate Oxidase with Inhibitor Compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: Y.43, Y.44, A.96, T.97, A.98, S.125, W.127, Q.147, Y.149, T.175, K.253, S.275, H.277, G.278, R.280, D.308, G.309, G.310, R.312, V.330, G.331, R.332 Ligands: YOJ.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.43, A:Y.44, A:T.97, A:R.332 Hydrogen bonds: A:A.96, A:A.98, A:Q.147, A:Y.149, A:T.175, A:K.253, A:K.253, A:S.275, A:G.278, A:G.310, A:G.331, A:R.332 Water bridges: A:A.96, A:H.277, A:D.308, A:G.309, A:V.311, A:R.312, A:R.332 Salt bridges: A:R.312, A:R.332

1 x YOJ: 5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid(Non-covalent)

YOJ.2: 19 residues within 4Å: Chain A: Y.43, A.98, M.99, S.126, W.127, A.128, T.129, S.130, S.131, Y.149, Y.151, V.156, R.184, L.222, Y.225, V.226, H.277, R.280 Ligands: FMN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.98, A:W.127, A:W.127, A:Y.225, A:V.226 Hydrogen bonds: A:W.127, A:E.134, A:Y.149 Salt bridges: A:R.184, A:H.277, A:R.280 pi-Stacking: A:Y.151

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

EDO.3: 3 residues within 4Å: Chain A: N.49, D.50, L.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.49, A:D.50 EDO.5: 6 residues within 4Å: Chain A: R.262, V.265, A.298, V.299, E.300, K.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.299 EDO.6: 2 residues within 4Å: Chain A: V.176, P.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.176 EDO.9: 3 residues within 4Å: Chain A: L.54, A.55, I.58 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.45, A:A.55

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: D.78, S.80, N.368, K.370 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.370 PEG.7: 7 residues within 4Å: Chain A: V.35, L.36, R.101, M.102, A.103, H.104, V.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.35 PEG.8: 4 residues within 4Å: Chain A: L.22, D.27, Q.30, H.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.30, A:Q.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, J. et al., Dual Glycolate Oxidase/Lactate Dehydrogenase A Inhibitors for Primary Hyperoxaluria. ACS Medicinal Chemistry Letters (2021)

Release Date

2021-07-14

Peptides

Hydroxyacid oxidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hydroxyacid oxidase 1

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