SMTL ID : 6rkq.1

Crystal Structure of TGT in complex with N2-methyl-8-(prop-1-yn-1-yl)-3H,7H,8H-imidazo[4,5-g]quinazoline-2,6-diamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 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.5: 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

2 x K75: (8~{R})-~{N}2-methyl-8-prop-1-ynyl-7,8-dihydro-3~{H}-imidazo[4,5-g]quinazoline-2,6-diamine(Non-covalent)

K75.2: 15 residues within 4Å: Chain A: D.93, S.94, G.96, Y.97, D.147, C.149, I.192, Q.194, G.220, G.221, L.222, A.223, V.224, M.251, G.252 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.194, A:M.251 Hydrogen bonds: A:S.94, A:Y.97, A:A.223 Water bridges: A:G.95, A:L.222, A:G.252, A:D.271 Salt bridges: A:D.93, A:D.147 pi-Stacking: A:Y.97, A:Y.97 K75.6: 15 residues within 4Å: Chain B: D.93, S.94, G.96, Y.97, D.147, C.149, I.192, Q.194, G.220, G.221, L.222, A.223, V.224, M.251, G.252 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Q.194, B:M.251 Hydrogen bonds: B:S.94, B:Y.97, B:A.223 Water bridges: B:G.95, B:L.222, B:G.252, B:D.271 Salt bridges: B:D.93, B:D.147 pi-Stacking: B:Y.97, B:Y.97

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.47, E.48, R.51, G.85, W.86, D.87, R.88 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.47, A:G.85, A:D.87, A:R.88 Water bridges: A:E.48, A:R.88 GOL.7: 7 residues within 4Å: Chain B: P.47, E.48, R.51, G.85, W.86, D.87, R.88 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.47, B:G.85, B:D.87, B:R.88 Water bridges: B:E.48, B:R.88

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

DMS.4: 6 residues within 4Å: Chain A: L.302, P.304, C.314, K.316, W.317, S.318 No protein-ligand interaction detected (PLIP) DMS.8: 6 residues within 4Å: Chain B: L.302, P.304, C.314, 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., Fragment Screening Hit Draws Attention to a Novel Transient Pocket Adjacent to the Recognition Site of the tRNA-Modifying Enzyme TGT. J.Med.Chem. (2020)

Release Date

2020-06-03

Peptides

Queuine tRNA-ribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Queuine tRNA-ribosyltransferase

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