SMTL ID : 6fiw.1

Human cytosolic 5'-nucleotidase II co-crystallized with 10mM Sodium ((4-(3'-((7H-purin-6-yl)carbamoyl)-[1,1'-biphenyl]-3-yl)-1H-imidazol-1-yl) methyl) phosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: N.250, H.352 Ligands: MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.250 Water bridges: A:D.52, A:D.54, A:T.249, A:K.292 SO4.2: 5 residues within 4Å: Chain A: R.144, K.362, Q.453, R.456, Y.457 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.453, A:Y.457 Salt bridges: A:R.144, A:K.362

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.52, D.54, D.351 Ligands: SO4.1 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.52, A:D.54, A:D.351, H2O.1, H2O.2, H2O.3

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.284, A:H.323, A:G.324, A:G.324, A:I.325 Water bridges: A:I.286 GOL.5: 7 residues within 4Å: Chain A: P.96, T.97, E.374, E.378, Y.434, G.438, L.440 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.96, A:E.378, A:Y.434, A:L.440 GOL.6: 5 residues within 4Å: Chain A: D.257, T.261, P.278, W.279, Q.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.257, A:W.279, A:Q.280 Water bridges: A:W.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guillon, R. et al., Lead optimization and biological evaluation of fragment-based cN-II inhibitors. Eur J Med Chem (2019)

Release Date

2019-01-30

Peptides

Cytosolic purine 5'-nucleotidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytosolic purine 5'-nucleotidase

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