SMTL ID : 6fiu.1

Human cytosolic 5'-nucleotidase II soaked with 10mM 2-(6-([1,1'-Biphenyl]-3-carboxamido)-9H-purin-9-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: N.250, H.352 Ligands: MG.14 8 PLIP interactions: 8 interactions with chain A Water bridges: A:D.52, A:D.54, A:D.54, A:T.155, A:T.155, A:K.292, A:D.351 Salt bridges: A:H.352 SO4.2: 3 residues within 4Å: Chain A: R.177, D.187, G.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.187 Water bridges: A:R.177 SO4.3: 4 residues within 4Å: Chain A: K.25, R.28, R.29, Y.475 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.475 Salt bridges: A:K.25, A:R.28 SO4.4: 5 residues within 4Å: Chain A: G.130, P.131, R.134, K.140 Ligands: SO4.7 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.134, A:K.140, A:K.424 SO4.5: 4 residues within 4Å: Chain A: R.144, Q.453, R.456, Y.457 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.453, A:Y.457, A:Y.457 Salt bridges: A:R.144, A:R.456 SO4.6: 3 residues within 4Å: Chain A: N.117, K.140, R.446 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.446 SO4.7: 6 residues within 4Å: Chain A: R.129, G.130, P.131, K.140, K.424 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.130 Salt bridges: A:K.140, A:K.424

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: R.76, W.207, K.211 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.76, A:R.76, A:K.211, A:K.211 GOL.9: 6 residues within 4Å: Chain A: P.96, T.97, E.374, E.378, Y.434, L.440 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.96, A:Y.434, A:L.440 Water bridges: A:E.374, A:E.374 GOL.10: 5 residues within 4Å: Chain A: D.257, T.261, P.278, W.279, Q.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.257, A:T.261, A:Q.280 GOL.11: 5 residues within 4Å: Chain A: R.39, K.344, K.361, R.367, D.459 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.361, A:R.367 GOL.12: 7 residues within 4Å: Chain A: D.252, Y.253, K.254, V.288, D.289, G.310, L.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.254, A:L.312 GOL.13: 9 residues within 4Å: Chain A: Q.280, F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.284, A:H.323, A:G.324 Water bridges: A:I.286

1 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 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

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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