SMTL ID : 4q4p.1

tRNA-Guanine Transglycosylase (TGT) in Complex with 2-{[2-(PIPERIDIN-1-YL)ETHYL]AMINO}-3,5-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.318, C.320, C.323, H.349 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.318, A:C.320, A:C.323, A:H.349 ZN.6: 4 residues within 4Å: Chain B: C.318, C.320, C.323, H.349 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.318, B:C.320, B:C.323, B:H.349

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: P.56, E.57, G.94, W.95, D.96, R.97 Chain B: K.325 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.94, A:D.96, A:R.97 Water bridges: B:K.325, B:K.325, B:K.325, B:K.325 GOL.7: 7 residues within 4Å: Chain A: K.325 Chain B: P.56, E.57, G.94, W.95, D.96, R.97 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: B:G.94, B:D.96, B:R.97 Water bridges: A:K.325, A:K.325, A:K.325, A:K.325

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

DMS.3: 3 residues within 4Å: Chain A: S.188, R.189, K.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.190 Water bridges: A:E.191 DMS.8: 3 residues within 4Å: Chain B: S.188, R.189, K.190 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.190 Water bridges: B:E.191

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: G.261, C.281, V.282 Ligands: 2YO.5 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: G.261, C.281, V.282 Ligands: 2YO.10 Ligand excluded by PLIP

2 x 2YO: 2-{[2-(PIPERIDIN-1-YL)ETHYL]AMINO}-3,5-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE(Non-covalent)

2YO.5: 16 residues within 4Å: Chain A: Y.106, D.156, C.158, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261, C.281, V.282, L.283, R.286 Ligands: CL.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.282, A:L.283 Hydrogen bonds: A:D.156, A:Q.203, A:G.230, A:A.232 Water bridges: A:C.158 pi-Stacking: A:Y.106 2YO.10: 16 residues within 4Å: Chain B: Y.106, D.156, C.158, Q.203, G.229, G.230, L.231, A.232, V.233, M.260, G.261, C.281, V.282, L.283, R.286 Ligands: CL.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.282, B:L.283 Hydrogen bonds: B:D.156, B:Q.203, B:G.230, B:A.232 Water bridges: B:C.158 pi-Stacking: B:Y.106

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Neeb, M. et al., Beyond Affinity: Enthalpy-Entropy Factorization Unravels Complexity of a Flat Structure-Activity Relationship for Inhibition of a tRNA-Modifying Enzyme. J.Med.Chem. (2014)

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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