SMTL ID : 4h4b.1 (1 other biounit)

Human cytosolic 5'-nucleotidase II in complex with Anthraquinone-2,6- disulfonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x 11H: 9,10-dioxo-9,10-dihydroanthracene-2,6-disulfonic acid(Non-covalent)

11H.1: 8 residues within 4Å: Chain A: R.163, I.171, N.173, K.311, P.312, H.371, F.373, Q.472 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.373 Hydrogen bonds: A:N.173, A:Q.472 Salt bridges: A:R.163 pi-Stacking: A:F.373, A:F.373 11H.9: 8 residues within 4Å: Chain B: R.163, I.171, N.173, K.311, P.312, H.371, F.373, Q.472 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.373 Hydrogen bonds: B:N.173, B:Q.472 Salt bridges: B:R.163 pi-Stacking: B:F.373, B:F.373 11H.17: 8 residues within 4Å: Chain C: R.163, I.171, N.173, K.311, P.312, H.371, F.373, Q.472 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.373 Hydrogen bonds: C:N.173, C:Q.472 Salt bridges: C:R.163 pi-Stacking: C:F.373, C:F.373 11H.25: 8 residues within 4Å: Chain D: R.163, I.171, N.173, K.311, P.312, H.371, F.373, Q.472 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.373 Hydrogen bonds: D:N.173, D:Q.472 Salt bridges: D:R.163 pi-Stacking: D:F.373, D:F.373

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.299, F.302, D.303, L.304, I.305, Q.341, H.342, G.343, I.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.305, A:G.343 GOL.10: 9 residues within 4Å: Chain B: Q.299, F.302, D.303, L.304, I.305, Q.341, H.342, G.343, I.344 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.305, B:G.343 GOL.18: 9 residues within 4Å: Chain C: Q.299, F.302, D.303, L.304, I.305, Q.341, H.342, G.343, I.344 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.305, C:H.342, C:G.343 GOL.26: 9 residues within 4Å: Chain D: Q.299, F.302, D.303, L.304, I.305, Q.341, H.342, G.343, I.344 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.305, D:H.342, D:G.343

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.71, D.73, T.75, D.370, D.375 Ligands: SO4.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:D.73, A:D.370, H2O.1, H2O.2 MG.11: 6 residues within 4Å: Chain B: D.71, D.73, T.75, D.370, D.375 Ligands: SO4.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.71, B:D.73, B:D.370, H2O.3, H2O.5 MG.19: 6 residues within 4Å: Chain C: D.71, D.73, T.75, D.370, D.375 Ligands: SO4.21 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.71, C:D.73, C:D.370, H2O.5, H2O.7 MG.27: 6 residues within 4Å: Chain D: D.71, D.73, T.75, D.370, D.375 Ligands: SO4.29 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.71, D:D.73, D:D.370, H2O.8, H2O.9

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

SO4.4: 8 residues within 4Å: Chain A: R.163, L.377, L.468, Q.472, R.475, Y.476 Chain C: K.381, R.475 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: N.269, H.371 Ligands: MG.3 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: R.95, W.226 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: G.149, P.150, R.153, K.159 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: N.136, L.137, K.159, R.465 Chain C: K.363 Ligand excluded by PLIP SO4.12: 8 residues within 4Å: Chain B: R.163, L.377, L.468, Q.472, R.475, Y.476 Chain D: K.381, R.475 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: N.269, H.371 Ligands: MG.11 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: R.95, W.226 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: G.149, P.150, R.153, K.159 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: N.136, L.137, K.159, R.465 Chain D: K.363 Ligand excluded by PLIP SO4.20: 8 residues within 4Å: Chain A: K.381, R.475 Chain C: R.163, L.377, L.468, Q.472, R.475, Y.476 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: N.269, H.371 Ligands: MG.19 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: R.95, W.226 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: G.149, P.150, R.153, K.159 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain A: K.363 Chain C: N.136, L.137, K.159, R.465 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain B: K.381, R.475 Chain D: R.163, L.377, L.468, Q.472, R.475, Y.476 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain D: N.269, H.371 Ligands: MG.27 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain D: R.95, W.226 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: G.149, P.150, R.153, K.159 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain B: K.363 Chain D: N.136, L.137, K.159, R.465 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jordheim, L.P. et al., Identification and characterization of inhibitors of cytoplasmic 5'-nucleotidase cN-II issued from virtual screening. Biochem Pharmacol (2013)

Release Date

2012-12-26

Peptides

Cytosolic purine 5'-nucleotidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Cytosolic purine 5'-nucleotidase

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