SMTL ID : 8ug1.1

Crystal structure of KHK-C and compound 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

2 x WNH: {(2R)-1-[(4M)-4-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-6-(trifluoromethyl)pyrimidin-2-yl]azetidin-2-yl}methanol(Non-covalent)

WNH.1: 19 residues within 4Å: Chain A: N.124, A.241, A.243, E.244, G.246, A.261, F.262, P.263, P.264, V.267, T.270, A.273, G.274, F.277, C.299, A.302, G.303, C.306 Chain B: D.44 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.241, A:A.243, A:F.277 Hydrogen bonds: A:A.273 WNH.6: 16 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, G.274, F.277, C.299, A.302, G.303, C.306 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.241, B:A.243, B:T.270, B:F.277 Hydrogen bonds: B:A.273 Water bridges: B:A.243

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

SO4.2: 2 residues within 4Å: Chain A: G.83, H.84 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.84 Water bridges: A:V.85 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.272, A:G.272, A:G.274, A:D.275 Salt bridges: A:R.125 SO4.7: 6 residues within 4Å: Chain A: R.48 Chain B: L.28, H.130, R.158, K.191, R.193 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Salt bridges: A:R.48, B:H.130, B:R.158, B:K.191, B:R.193 Water bridges: B:K.191, B:K.191, B:R.193 SO4.8: 2 residues within 4Å: Chain B: R.296, Q.300 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.300, B:Q.300 Salt bridges: B:R.296 SO4.9: 3 residues within 4Å: Chain B: K.210, K.214, W.242 3 PLIP interactions: 3 interactions with chain B Water bridges: B:W.242 Salt bridges: B:K.210, B:K.214 SO4.10: 5 residues within 4Å: Chain B: R.95, R.96, G.310, F.311 Ligands: GOL.12 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.311 Water bridges: B:R.95, B:R.95, B:R.95, B:R.96 Salt bridges: B:R.95, B:R.96 SO4.11: 4 residues within 4Å: Chain A: W.54 Chain B: G.83, H.84, V.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.84, B:V.85 Water bridges: B:A.86

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: V.30, D.32, G.57, G.58, N.59, N.62, S.114, I.127, L.271 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.58, A:N.62, A:S.114, A:S.114 Water bridges: A:D.32, A:D.32, A:N.59, A:N.59 GOL.12: 7 residues within 4Å: Chain B: Q.55, R.56, G.57, N.62, G.310, F.311 Ligands: SO4.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.56, B:N.62 Water bridges: B:Q.55, B:Q.55, B:G.58, B:D.92, B:G.310 GOL.13: 4 residues within 4Å: Chain B: F.283, S.284, R.289, F.297 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: 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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