SMTL ID : 6mkm.1

Crystallographic solvent mapping analysis of DMSO/Tris bound to APE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 5 residues within 4Å: Chain A: D.37, E.63, K.65, Y.138, D.275 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.63, A:K.65, A:Y.138, A:D.275 Water bridges: A:N.35, A:N.35, A:N.35, A:D.37, A:D.37

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

DMS.2: 6 residues within 4Å: Chain A: N.141, N.179, A.197, F.233, W.247, L.249 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.141 Water bridges: A:G.143 pi-Cation interactions: A:W.247, A:W.247 DMS.3: 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

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

EDO.4: 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:R.204 EDO.5: 5 residues within 4Å: Chain A: E.68, W.86, S.87, A.88, Y.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.68, A:A.88, A:A.88

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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