SMTL ID : 3kbi.1

Crystal Structure of Human PL Kinase with bound Theophylline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 1 residues within 4Å: Chain A: D.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.113 Water bridges: A:N.150, A:N.150, A:G.234 NA.10: 0 residues within 4Å: (No contacts) 4 PLIP interactions: 4 interactions with chain B Water bridges: B:D.113, B:N.150, B:N.150, B:E.153

1 x TEP: THEOPHYLLINE(Non-covalent)

TEP.2: 8 residues within 4Å: Chain A: S.12, G.20, F.43, H.46, T.47, Y.84, V.231, D.235 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.12, A:T.47 Water bridges: A:S.12, A:S.12, A:Y.84, A:D.235, A:D.235, A:D.235

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

MPD.3: 5 residues within 4Å: Chain A: T.186, T.233, G.234, F.237, L.263 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.237 Hydrogen bonds: A:T.233 MPD.4: 4 residues within 4Å: Chain A: K.76, Y.77, D.78, N.105 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.76, A:N.105 Hydrogen bonds: A:K.76, A:N.105 Water bridges: A:N.105, A:R.107 MPD.5: 5 residues within 4Å: Chain A: I.223, R.224, K.225, V.226, H.264 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.223, A:V.226 MPD.6: 5 residues within 4Å: Chain A: C.5, L.31, G.32, F.33, K.247 No protein-ligand interaction detected (PLIP) MPD.11: 4 residues within 4Å: Chain B: D.181, R.206, R.207, R.208 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.181, B:R.208 MPD.12: 3 residues within 4Å: Chain B: M.126, E.130, L.156 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.156 Hydrogen bonds: B:E.130 Water bridges: B:M.126 MPD.13: 6 residues within 4Å: Chain B: S.12, V.19, H.46, T.47, Y.84 Ligands: MPD.14 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.19, B:Y.84 Hydrogen bonds: B:S.12, B:S.12, B:T.47, B:T.47 Water bridges: B:Y.84, B:Y.84 MPD.14: 5 residues within 4Å: Chain B: F.43, W.52, Y.84, R.86 Ligands: MPD.13 No protein-ligand interaction detected (PLIP) MPD.15: 6 residues within 4Å: Chain B: T.186, L.199, T.233, G.234, F.237 Ligands: MPD.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.237 MPD.16: 4 residues within 4Å: Chain B: V.109, Q.205, T.245, P.249 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.109, B:P.249 Hydrogen bonds: B:T.245 Water bridges: B:Y.79 MPD.17: 7 residues within 4Å: Chain B: I.223, R.224, V.226, H.264, L.267 Ligands: MPD.15, MPD.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.224, B:H.264, B:L.267 Hydrogen bonds: B:R.224, B:H.264 MPD.18: 7 residues within 4Å: Chain B: D.222, I.223, R.224, H.264, V.306, V.307 Ligands: MPD.17 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.223, B:V.307

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

SO4.7: 2 residues within 4Å: Chain A: L.156, K.161 No protein-ligand interaction detected (PLIP) SO4.8: 6 residues within 4Å: Chain A: Q.63, R.70, M.93, D.96, I.97, E.100 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.70 SO4.9: 7 residues within 4Å: Chain A: S.40, V.56, L.57, T.85, R.86, D.87, F.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.40, A:L.57, A:R.86, A:D.87 SO4.19: 5 residues within 4Å: Chain B: Q.63, Y.66, M.93, D.96, E.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63, B:D.96 Water bridges: B:D.96 SO4.20: 4 residues within 4Å: Chain B: E.4, C.5, D.78, H.246 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.78 Salt bridges: B:H.246 SO4.21: 6 residues within 4Å: Chain B: C.5, L.31, G.32, F.33, H.246, K.247 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.5 Salt bridges: B:H.246, B:K.247 SO4.22: 4 residues within 4Å: Chain B: E.155, L.156, G.159, R.160 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandhi, A.K. et al., Pyridoxal Kinase Inhibitors: Investigation of Inhibition and Binding Modes. To be Published

Release Date

2010-07-14

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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