SMTL ID : 5sw3.1

Crystal Structure of TGT in complex with 3-Pyridinecarboxylic acid, 6-(dimethylamino)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.309, C.311, V.313, C.314, H.340 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.309, A:C.311, A:C.314, A:H.340 ZN.9: 5 residues within 4Å: Chain B: C.309, C.311, V.313, C.314, H.340 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.309, B:C.311, B:C.314, B:H.340

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

DMS.2: 2 residues within 4Å: Chain A: E.110, R.168 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.110 DMS.3: 7 residues within 4Å: Chain A: P.47, E.48, R.51, G.85, W.86, D.87, R.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.87 Salt bridges: A:D.87 DMS.4: 4 residues within 4Å: Chain A: H.136, L.137, G.139, E.182 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.182 DMS.10: 2 residues within 4Å: Chain B: E.110, R.168 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.110 DMS.11: 7 residues within 4Å: Chain B: P.47, E.48, R.51, G.85, W.86, D.87, R.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.87 Salt bridges: B:D.87 DMS.12: 4 residues within 4Å: Chain B: H.136, L.137, G.139, E.182 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.182

4 x 46L: 6-(dimethylamino)pyridine-3-carboxylic acid(Non-covalent)

46L.5: 12 residues within 4Å: Chain A: Y.97, D.147, C.149, I.192, Q.194, G.220, G.221, L.222, A.223, V.224, M.251, G.252 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.97 Hydrogen bonds: A:Q.194, A:G.221 Water bridges: A:Y.97, A:D.147 pi-Stacking: A:Y.97 46L.6: 9 residues within 4Å: Chain A: M.66, A.71, E.72, H.124, M.125, R.130, E.133, I.134, L.137 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.134 Hydrogen bonds: A:M.125, A:M.125 Salt bridges: A:H.124 46L.13: 12 residues within 4Å: Chain B: Y.97, D.147, C.149, I.192, Q.194, G.220, G.221, L.222, A.223, V.224, M.251, G.252 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.97 Hydrogen bonds: B:Q.194, B:G.221 Water bridges: B:Y.97, B:D.147 pi-Stacking: B:Y.97 46L.14: 9 residues within 4Å: Chain B: M.66, A.71, E.72, H.124, M.125, R.130, E.133, I.134, L.137 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.134 Hydrogen bonds: B:M.125, B:M.125 Salt bridges: B:H.124

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: W.287, E.308, K.351, F.364, R.371 No protein-ligand interaction detected (PLIP) PEG.15: 5 residues within 4Å: Chain B: W.287, E.308, K.351, F.364, R.371 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 8 residues within 4Å: Chain A: L.302, P.304, C.314, Q.315, K.316, W.317, S.318 Chain B: S.82 No protein-ligand interaction detected (PLIP) PG4.16: 8 residues within 4Å: Chain A: S.82 Chain B: L.302, P.304, C.314, Q.315, K.316, W.317, S.318 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hassaan, E. et al., Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. Chemmedchem (2020)

Release Date

2017-07-19

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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