SMTL ID : 4q4o.1

tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2-(piperidin-1-yl)ethyl]amino}-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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.7: 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 DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 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

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.94, A:D.96, A:R.97, B:K.325 Water bridges: A:E.57, A:R.97, B:K.325 GOL.4: 7 residues within 4Å: Chain A: W.296, E.317, K.360, F.373, D.376, F.377, R.380 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.317, A:K.360, A:D.376, A:R.380 Water bridges: A:E.317 GOL.9: 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: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.94, B:D.96, B:R.97, A:K.325 Water bridges: B:E.57, B:R.97, A:K.325 GOL.10: 7 residues within 4Å: Chain B: W.296, E.317, K.360, F.373, D.376, F.377, R.380 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.317, B:K.360, B:D.376, B:R.380 Water bridges: B:K.360

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

CL.5: 3 residues within 4Å: Chain A: C.281, V.282 Ligands: 2YM.6 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: C.281, V.282 Ligands: 2YM.12 Ligand excluded by PLIP

2 x 2YM: 6-amino-2-{[2-(piperidin-1-yl)ethyl]amino}-3,5-dihydro-8H-imidazo[4,5-g]quinazolin-8-one(Non-covalent)

2YM.6: 17 residues within 4Å: Chain A: D.102, S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, C.281, V.282, R.286 Ligands: CL.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.106, A:M.260, A:V.282 Hydrogen bonds: A:S.103, A:Y.106, A:Q.203, A:G.230, A:A.232 Water bridges: A:L.231 Salt bridges: A:D.102, A:D.156 pi-Stacking: A:Y.106, A:Y.106 2YM.12: 17 residues within 4Å: Chain B: D.102, S.103, Y.106, D.156, C.158, I.201, Q.203, G.229, G.230, L.231, A.232, M.260, G.261, C.281, V.282, R.286 Ligands: CL.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.106, B:M.260, B:V.282 Hydrogen bonds: B:S.103, B:Y.106, B:Q.203, B:G.230, B:A.232 Water bridges: B:L.231 Salt bridges: B:D.102, B:D.156 pi-Stacking: B:Y.106, B:Y.106

Links

RCSB   PDBe   PDBe-KB   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)

Release Date

2014-07-09

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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