SMTL ID : 8wr2.1

Crystal Structure of Human Pyridoxal Kinase with bound Luteolin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 7 residues within 4Å: Chain A: K.297, R.298 Chain B: V.30, L.31, W.244, K.247, E.301 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.297, A:K.297, A:R.298, B:E.301 Water bridges: A:K.297, B:V.30 Salt bridges: B:K.247 GLC-GLC.2: 6 residues within 4Å: Chain A: V.30, L.31, W.244, K.247, E.301 Chain B: K.297 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.297, B:K.297 Water bridges: B:K.297, A:V.30, A:E.301 Salt bridges: B:K.297, A:K.247

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: D.113, T.148 Ligands: LU2.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.113, A:T.148 Water bridges: A:N.150 NA.10: 4 residues within 4Å: Chain B: D.113, T.148, T.186 Ligands: LU2.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.186 Water bridges: B:N.150

2 x LU2: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one(Non-covalent)

LU2.4: 13 residues within 4Å: Chain A: T.186, L.199, I.223, K.225, V.226, T.233, G.234, F.237, V.260, L.263, H.264, L.267 Ligands: NA.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.186, A:T.233, A:F.237, A:F.237, A:F.237 Hydrogen bonds: A:V.226 Water bridges: A:N.150, A:V.226, A:T.233, A:T.233, A:G.234 LU2.11: 13 residues within 4Å: Chain B: T.186, I.223, R.224, K.225, V.226, T.233, G.234, F.237, V.260, L.263, H.264, L.267 Ligands: NA.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.233, B:F.237, B:F.237 Hydrogen bonds: B:V.226, B:V.226 Water bridges: B:N.150, B:E.153, B:S.187, B:S.187, B:H.264

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 5 residues within 4Å: Chain A: S.12, V.19, H.46, T.47, Y.84 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.19, A:Y.84, A:Y.84 Hydrogen bonds: A:T.47 MPD.6: 7 residues within 4Å: Chain A: G.124, S.125, M.126, E.130, F.152, L.156 Ligands: MPD.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.152, A:L.156 MPD.7: 5 residues within 4Å: Chain A: E.155, G.159, R.160, K.161 Ligands: MPD.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.155, A:G.159 MPD.12: 8 residues within 4Å: Chain B: S.12, V.14, V.19, V.41, F.43, H.46, T.47, Y.84 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.14, B:V.41, B:F.43, B:Y.84 Hydrogen bonds: B:T.47 MPD.13: 3 residues within 4Å: Chain B: M.126, E.130 Ligands: MPD.14 No protein-ligand interaction detected (PLIP) MPD.14: 7 residues within 4Å: Chain B: F.152, E.155, L.156, G.159, R.160, K.161 Ligands: MPD.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.152, B:K.161 Hydrogen bonds: B:K.161, B:K.161

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 2 residues within 4Å: Chain A: D.181, R.208 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.181 DMS.9: 3 residues within 4Å: Chain A: Q.63, R.70, E.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.70 Salt bridges: A:E.100 DMS.15: 3 residues within 4Å: Chain B: D.181, R.206, R.208 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.206 Salt bridges: B:D.181 DMS.16: 3 residues within 4Å: Chain B: Q.63, Y.66, E.100 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Y. et al., Discovery and characterization of natural product luteolin as an effective inhibitor of human pyridoxal kinase. Bioorg.Chem. (2024)

Release Date

2024-03-20

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Pyridoxal kinase

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