SMTL ID : 6fso.1

Crystal Structure of TGT in complex with methyl({[5-(pyridin-3-yloxy)furan-2-yl]methyl})amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 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.10: 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 9 residues within 4Å: Chain A: K.24, R.25, G.139, S.140, D.141, E.182, Q.183, N.186, A.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.141 Water bridges: A:N.186 PEG.3: 3 residues within 4Å: Chain A: R.294, R.327 Chain B: R.68 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.294, A:R.327, B:R.68 Water bridges: A:H.323 PEG.4: 6 residues within 4Å: Chain A: P.240, M.241, L.242, P.243, D.244, D.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.241, A:D.244, A:D.245, A:D.245 PEG.11: 9 residues within 4Å: Chain B: K.24, R.25, G.139, S.140, D.141, E.182, Q.183, N.186, A.187 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.186 PEG.12: 3 residues within 4Å: Chain A: R.68 Chain B: R.294, R.327 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.294, B:R.327, A:R.68 Water bridges: B:H.323 PEG.13: 6 residues within 4Å: Chain B: P.240, M.241, L.242, P.243, D.244, D.245 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.241, B:D.244, B:D.245, B:D.245

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

DMS.5: 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.14: 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

2 x F63: N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine(Non-covalent)

F63.6: 6 residues within 4Å: Chain A: M.163, E.164, M.167, R.168, Q.204, A.208 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.204 Hydrogen bonds: A:E.164, A:R.168, A:Q.204 F63.15: 6 residues within 4Å: Chain B: M.163, E.164, M.167, R.168, Q.204, A.208 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.204 Hydrogen bonds: B:E.164, B:E.164, B:R.168, B:Q.204

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

PG4.7: 10 residues within 4Å: Chain A: W.287, E.308, C.309, H.310, Q.347, Q.350, K.351, F.364, F.368, R.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.351 Water bridges: A:R.371 PG4.16: 10 residues within 4Å: Chain B: W.287, E.308, C.309, H.310, Q.347, Q.350, K.351, F.364, F.368, R.371 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.351 Water bridges: B:R.371

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 6 residues within 4Å: Chain A: V.36, K.43, V.273, T.276, R.277, R.280 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.36, A:V.273 Hydrogen bonds: A:T.276 Salt bridges: A:K.43, A:R.277, A:R.280 ACT.17: 6 residues within 4Å: Chain B: V.36, K.43, V.273, T.276, R.277, R.280 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.36, B:V.273 Hydrogen bonds: B:T.276 Salt bridges: B:K.43, B:R.277, B:R.280

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 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) PGE.18: 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

2019-03-20

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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