SMTL ID : 8i6b.1

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ODF: 5-oxidanyl-1~{H}-pyrimidine-2,4-dione(Non-covalent)

ODF.1: 9 residues within 4Å: Chain A: G.77, Q.78, D.79, P.80, Y.81, S.91, F.92, N.138, H.202 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.78, A:D.79, A:F.92, A:N.138, A:N.138, A:H.202 Water bridges: A:Y.81, A:Y.81 pi-Stacking: A:Y.81, A:F.92

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: E.19, L.20, V.21, E.22, T.65 No protein-ligand interaction detected (PLIP)

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

DMS.3: 2 residues within 4Å: Chain A: G.50, R.52 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.52 DMS.4: 3 residues within 4Å: Chain A: T.65, F.66, P.67 No protein-ligand interaction detected (PLIP) DMS.5: 3 residues within 4Å: Chain A: I.47, R.52, Y.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.53 pi-Cation interactions: A:Y.53 DMS.6: 2 residues within 4Å: Chain A: Q.131, R.132 No protein-ligand interaction detected (PLIP) DMS.7: 5 residues within 4Å: Chain A: Q.78, H.202, S.204, L.206, S.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.204 Water bridges: A:Q.78 pi-Cation interactions: A:H.202

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 6 residues within 4Å: Chain A: F.66, P.67, N.70, V.71, G.133 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.130 Water bridges: A:G.133

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

CL.9: 5 residues within 4Å: Chain A: F.66, A.130, V.134, L.135 Ligands: NA.8 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: R.51, R.52, R.144 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: E.223, G.227 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kesharwani, S. et al., Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment. Eur.J.Med.Chem. (2023)

Release Date

2023-07-12

Peptides

Uracil-DNA glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uracil-DNA glycosylase

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