SMTL ID : 6mk3.1

Crystallographic solvent mapping analysis of DMSO bound to APE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

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

DMS.1: 6 residues within 4Å: Chain A: N.141, N.179, A.197, F.233, W.247, L.249 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.141 pi-Cation interactions: A:W.247 DMS.2: 6 residues within 4Å: Chain A: Q.104, A.105, P.106, L.107, F.129, D.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.130 Water bridges: A:S.131 Salt bridges: A:D.130

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.183, A:G.208 EDO.4: 6 residues within 4Å: Chain A: Y.12, W.234, R.241, N.244, S.269, K.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.12, A:R.241, A:S.269 Water bridges: A:Y.12, A:N.244 EDO.5: 6 residues within 4Å: Chain A: K.45, Y.236, R.241, L.272, G.273, S.274 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.45, A:K.45, A:Y.236, A:R.241, A:G.273, A:S.274 Water bridges: A:R.241, A:A.271

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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