SMTL ID : 6fis.1

Human cytosolic 5'-nucleotidase II soaked with 10mM 7-Benzyloxymethyl-7H-adenine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.25, R.28, Y.475 Ligand excluded by PLIP SO4.2: 4 residues within 4Å: Chain A: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: N.250, H.352 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain A: R.144, L.358, K.362, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.117, K.140, R.446 Chain C: K.344 Ligand excluded by PLIP SO4.9: 7 residues within 4Å: Chain A: T.104, T.147, E.148, R.149, R.195, F.198, Q.199 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: K.25, R.28, Y.475 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: N.250, H.352 Ligand excluded by PLIP SO4.16: 6 residues within 4Å: Chain B: R.144, L.358, K.362, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: N.117, K.140, R.446 Chain D: K.344 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain B: T.104, T.147, E.148, R.149, R.195, F.198, Q.199 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain C: K.25, R.28, Y.475 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain C: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.21: 2 residues within 4Å: Chain C: N.250, H.352 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain C: R.144, L.358, K.362, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: K.344 Chain C: N.117, K.140, R.446 Ligand excluded by PLIP SO4.27: 7 residues within 4Å: Chain C: T.104, T.147, E.148, R.149, R.195, F.198, Q.199 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain D: K.25, R.28, Y.475 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain D: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain D: N.250, H.352 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain D: R.144, L.358, K.362, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain B: K.344 Chain D: N.117, K.140, R.446 Ligand excluded by PLIP SO4.36: 7 residues within 4Å: Chain D: T.104, T.147, E.148, R.149, R.195, F.198, Q.199 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.76, W.207, K.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.76, A:R.76, A:K.211 GOL.6: 8 residues within 4Å: Chain A: 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:I.286, A:H.323, A:G.324 GOL.13: 3 residues within 4Å: Chain B: R.76, W.207, K.211 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.76, B:R.76, B:K.211 GOL.15: 8 residues within 4Å: Chain B: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.284, B:I.286, B:H.323, B:G.324 GOL.22: 3 residues within 4Å: Chain C: R.76, W.207, K.211 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.76, C:R.76, C:K.211 GOL.24: 8 residues within 4Å: Chain C: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.284, C:I.286, C:H.323, C:G.324 GOL.31: 3 residues within 4Å: Chain D: R.76, W.207, K.211 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.76, D:R.76, D:K.211 GOL.33: 8 residues within 4Å: Chain D: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.284, D:I.286, D:H.323, D:G.324

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.52, D.54, D.351 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.52, A:D.54, A:D.351, H2O.3, H2O.3, H2O.4 MG.14: 3 residues within 4Å: Chain B: D.52, D.54, D.351 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.52, B:D.54, B:D.351, H2O.11, H2O.11, H2O.12 MG.23: 3 residues within 4Å: Chain C: D.52, D.54, D.351 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.52, C:D.54, C:D.351, H2O.19, H2O.20, H2O.20 MG.32: 3 residues within 4Å: Chain D: D.52, D.54, D.351 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.52, D:D.54, D:D.351, H2O.28, H2O.28, H2O.29

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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