SMTL ID : 6mkk.1

Crystallographic solvent mapping analysis of DMSO/Mg bound to APE1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.37, E.63 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.37, A:E.63, H2O.1, H2O.1, H2O.2, H2O.7

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

DMS.2: 6 residues within 4Å: Chain A: N.141, A.197, G.198, F.233, W.247, L.249 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.247, A:W.247

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

EDO.3: 5 residues within 4Å: Chain A: H.182, E.183, R.204, Q.205, G.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.183, A:G.208 Water bridges: A:R.204 EDO.4: 2 residues within 4Å: Chain A: K.45, Y.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.45 Water bridges: A:Y.236 EDO.5: 4 residues within 4Å: Chain A: S.82, H.83, Q.84, Y.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.83, A:Q.84, A:Q.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trilles, R. et al., Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1. J. Med. Chem. (2019)

Release Date

2019-01-30

Peptides

DNA-(apurinic or apyrimidinic site) lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-(apurinic or apyrimidinic site) lyase

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