SMTL ID : 6fxh.1

Human cytosolic 5'-nucleotidase II soaked with 10mM 3-Phenyl-N-(9H-purin-6-yl)benzamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.25, R.28, Y.475 Chain C: K.404 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 SO4.4: 4 residues within 4Å: Chain A: R.144, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: R.129, G.130, P.131, K.140, K.424 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: K.25, R.28, Y.475 Chain D: K.404 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: N.250, H.352 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: R.144, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: R.129, G.130, P.131, K.140, K.424 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain A: K.404 Chain C: K.25, R.28, Y.475 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain C: N.250, H.352 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: R.144, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain C: R.129, G.130, P.131, K.140, K.424 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain B: K.404 Chain D: K.25, R.28, Y.475 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain D: G.130, P.131, R.134, K.140 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain D: N.250, H.352 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain D: R.144, Q.453, R.456, Y.457 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain D: R.129, G.130, P.131, K.140, K.424 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 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.1, H2O.2, H2O.3 MG.7: 2 residues within 4Å: Chain A: R.446 Chain C: K.344 No protein-ligand interaction detected (PLIP) MG.17: 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.10, H2O.11, H2O.12 MG.18: 2 residues within 4Å: Chain B: R.446 Chain D: K.344 No protein-ligand interaction detected (PLIP) MG.28: 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.29: 2 residues within 4Å: Chain A: K.344 Chain C: R.446 No protein-ligand interaction detected (PLIP) MG.39: 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.27, H2O.28, H2O.29 MG.40: 2 residues within 4Å: Chain B: K.344 Chain D: R.446 No protein-ligand interaction detected (PLIP)

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: Q.280, S.281, F.283, D.284, I.286, Q.322, H.323, G.324, I.325 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: S.93, P.96, T.97, E.374, E.378, Y.434, G.438, L.440 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: D.7, P.63, E.64 Ligand excluded by PLIP GOL.11: 8 residues within 4Å: Chain A: D.252, Y.253, V.288, D.289, V.305, G.310, K.311, L.312 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain B: Q.280, S.281, F.283, D.284, I.286, Q.322, H.323, G.324, I.325 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain B: S.93, P.96, T.97, E.374, E.378, Y.434, G.438, L.440 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain B: D.7, P.63, E.64 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: D.252, Y.253, V.288, D.289, V.305, G.310, K.311, L.312 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain C: Q.280, S.281, F.283, D.284, I.286, Q.322, H.323, G.324, I.325 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain C: S.93, P.96, T.97, E.374, E.378, Y.434, G.438, L.440 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain C: D.7, P.63, E.64 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain C: D.252, Y.253, V.288, D.289, V.305, G.310, K.311, L.312 Ligand excluded by PLIP GOL.41: 9 residues within 4Å: Chain D: Q.280, S.281, F.283, D.284, I.286, Q.322, H.323, G.324, I.325 Ligand excluded by PLIP GOL.42: 8 residues within 4Å: Chain D: S.93, P.96, T.97, E.374, E.378, Y.434, G.438, L.440 Ligand excluded by PLIP GOL.43: 3 residues within 4Å: Chain D: D.7, P.63, E.64 Ligand excluded by PLIP GOL.44: 8 residues within 4Å: Chain D: D.252, Y.253, V.288, D.289, V.305, G.310, K.311, L.312 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

2019-03-06

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