SMTL ID : 5np8.1

PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 93T: 3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid(Non-covalent)

93T.1: 10 residues within 4Å: Chain A: G.241, G.242, L.260, F.295, G.316, L.317, D.318, V.343, G.344, V.345 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.260, A:L.260, A:L.317, A:V.345 pi-Stacking: A:F.295

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

EDO.2: 4 residues within 4Å: Chain A: V.103, K.149, A.152, F.153 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.156 EDO.3: 4 residues within 4Å: Chain A: K.9, D.415, A.416, L.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.9, A:A.416 EDO.4: 4 residues within 4Å: Chain A: W.339, G.341, P.342, M.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.341, A:G.341

1 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.5: 8 residues within 4Å: Chain A: D.27, N.29, R.42, H.66, R.69, R.126, G.170, R.174 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.27, A:N.29, A:R.42, A:R.42, A:G.399 Water bridges: A:R.126, A:R.126, A:H.173, A:R.174, A:G.400 Salt bridges: A:R.42, A:H.66, A:R.69, A:R.126, A:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bilsland, A.E. et al., A Novel Pyrazolopyrimidine Ligand of Human PGK1 and Stress Sensor DJ1 Modulates the Shelterin Complex and Telomere Length Regulation. Neoplasia (2019)

Release Date

2018-05-16

Peptides

Phosphoglycerate kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglycerate kinase 1

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