SMTL ID : 6fir.1

Human cytosolic 5'-nucleotidase II soaked with 5mM3-Phenyl-N-(9H-purin-6-yl)benzamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.71, D.73, D.370 Ligands: SO4.2 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.71, A:D.73, A:D.370, H2O.1, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain B: D.71, D.73, D.370 Ligands: SO4.13 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.71, B:D.73, B:D.370, H2O.4, H2O.4, H2O.4 MG.23: 4 residues within 4Å: Chain C: D.71, D.73, D.370 Ligands: SO4.24 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.71, C:D.73, C:D.370, H2O.6, H2O.7, H2O.7 MG.34: 4 residues within 4Å: Chain D: D.71, D.73, D.370 Ligands: SO4.35 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.71, D:D.73, D:D.370, H2O.9, H2O.10, H2O.10

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

SO4.2: 4 residues within 4Å: Chain A: F.176, N.269, H.371 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.269 Water bridges: A:D.71, A:D.71, A:D.73, A:D.73 SO4.3: 5 residues within 4Å: Chain A: R.163, Q.472, R.475, Y.476 Chain C: R.475 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.472, A:Y.476, A:Y.476 Salt bridges: A:R.163, A:R.475, C:R.475 SO4.4: 4 residues within 4Å: Chain A: G.149, P.150, R.153, K.159 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.153, A:K.159, A:K.443 SO4.13: 4 residues within 4Å: Chain B: F.176, N.269, H.371 Ligands: MG.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.269 Water bridges: B:D.71, B:D.71, B:D.73, B:D.73 SO4.14: 5 residues within 4Å: Chain B: R.163, Q.472, R.475, Y.476 Chain D: R.475 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.472, B:Y.476, B:Y.476 Salt bridges: B:R.163, B:R.475, D:R.475 SO4.15: 4 residues within 4Å: Chain B: G.149, P.150, R.153, K.159 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.153, B:K.159, B:K.443 SO4.24: 4 residues within 4Å: Chain C: F.176, N.269, H.371 Ligands: MG.23 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.269 Water bridges: C:D.71, C:D.71, C:D.71, C:D.71 SO4.25: 5 residues within 4Å: Chain A: R.475 Chain C: R.163, Q.472, R.475, Y.476 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.472, C:Y.476 Salt bridges: C:R.163, C:R.475, A:R.475 SO4.26: 4 residues within 4Å: Chain C: G.149, P.150, R.153, K.159 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.153, C:K.159, C:K.443 SO4.35: 4 residues within 4Å: Chain D: F.176, N.269, H.371 Ligands: MG.34 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.269 Water bridges: D:D.71, D:D.71, D:D.71, D:D.71 SO4.36: 5 residues within 4Å: Chain B: R.475 Chain D: R.163, Q.472, R.475, Y.476 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.472, D:Y.476 Salt bridges: D:R.163, D:R.475, B:R.475 SO4.37: 4 residues within 4Å: Chain D: G.149, P.150, R.153, K.159 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.153, D:K.159, D:K.443

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.115, T.116, E.393, E.397, Y.453 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: L.28, V.78, V.246, D.248, A.482, S.483 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: D.271, Y.272, V.307, D.308, G.329, L.331, S.347 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: M.62, R.257, V.261, L.487, L.488, Y.490, F.492 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: R.53, V.54, V.56, Y.494, L.495, F.496, R.497 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: S.23, D.26, K.80, S.81, P.82, E.83 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: P.115, T.116, E.393, E.397, Y.453 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: L.28, V.78, V.246, D.248, A.482, S.483 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: D.271, Y.272, V.307, D.308, G.329, L.331, S.347 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: M.62, R.257, V.261, L.487, L.488, Y.490, F.492 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: R.53, V.54, V.56, Y.494, L.495, F.496, R.497 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: S.23, D.26, K.80, S.81, P.82, E.83 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: P.115, T.116, E.393, E.397, Y.453 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain C: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: L.28, V.78, V.246, D.248, A.482, S.483 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain C: D.271, Y.272, V.307, D.308, G.329, L.331, S.347 Ligand excluded by PLIP GOL.31: 7 residues within 4Å: Chain C: M.62, R.257, V.261, L.487, L.488, Y.490, F.492 Ligand excluded by PLIP GOL.32: 7 residues within 4Å: Chain C: R.53, V.54, V.56, Y.494, L.495, F.496, R.497 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain C: S.23, D.26, K.80, S.81, P.82, E.83 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain D: P.115, T.116, E.393, E.397, Y.453 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain D: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain D: L.28, V.78, V.246, D.248, A.482, S.483 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain D: D.271, Y.272, V.307, D.308, G.329, L.331, S.347 Ligand excluded by PLIP GOL.42: 7 residues within 4Å: Chain D: M.62, R.257, V.261, L.487, L.488, Y.490, F.492 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain D: R.53, V.54, V.56, Y.494, L.495, F.496, R.497 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: S.23, D.26, K.80, S.81, P.82, E.83 Ligand excluded by PLIP

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: 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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