SMTL ID : 8ug3.1

Crystal structure of KHK-C and compound 23

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x WRE: 2-[(4P)-4-{2-[(2S)-2-methylazetidin-1-yl]-6-(trifluoromethyl)pyrimidin-4-yl}-1H-pyrazol-1-yl]-1-(piperazin-1-yl)ethan-1-one(Non-covalent)

WRE.1: 17 residues within 4Å: Chain A: R.125, D.211, A.241, A.243, E.244, G.246, A.261, F.262, P.263, P.264, V.267, T.270, F.277, C.299, G.303, C.306 Chain B: D.44 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.243, A:F.277, A:F.277 Hydrogen bonds: B:D.44 WRE.5: 15 residues within 4Å: Chain B: A.241, A.243, E.244, G.246, A.261, F.262, P.263, P.264, T.270, A.273, F.277, C.299, A.302, G.303, C.306 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.243, B:F.277

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: G.83, H.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.84 Salt bridges: A:H.84 SO4.3: 3 residues within 4Å: Chain A: K.210, K.214, W.242 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.210, A:K.214 SO4.4: 6 residues within 4Å: Chain A: R.125, T.270, G.272, A.273, G.274, D.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.272, A:A.273, A:G.274, A:D.275, A:D.275 Salt bridges: A:R.125 SO4.6: 7 residues within 4Å: Chain A: R.48 Chain B: L.28, L.129, H.130, R.158, K.191, R.193 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Water bridges: B:K.191, B:K.191 Salt bridges: B:H.130, B:R.158, B:K.191, B:R.193, A:R.48 SO4.7: 2 residues within 4Å: Chain B: R.296, Q.300 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.300 Salt bridges: B:R.296 SO4.8: 4 residues within 4Å: Chain B: K.210, K.214, Q.219, W.242 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.210, B:K.214 SO4.9: 4 residues within 4Å: Chain B: R.95, R.96, G.310, F.311 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.311, B:D.312 Water bridges: B:R.96 Salt bridges: B:R.95, B:R.96

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain B: G.83, H.84, V.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.84, B:V.85 Water bridges: B:P.82, B:A.86 GOL.11: 5 residues within 4Å: Chain B: F.283, S.284, Q.287, R.289, F.297 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.284, B:Q.287, B:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Durham, T.B. et al., Identification of LY3522348: A Highly Selective and Orally Efficacious Ketohexokinase Inhibitor. J.Med.Chem. (2023)

Release Date

2023-12-06

Peptides

Ketohexokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketohexokinase

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