- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x 5WO: ~{N}-(7~{H}-purin-6-yl)-3-(3-pyrrol-1-ylphenyl)benzamide(Non-covalent)
- 20 x ACT: ACETATE ION(Non-functional Binders)
ACT.2: 3 residues within 4Å:- Chain A: K.258, E.259, G.261
Ligand excluded by PLIPACT.3: 5 residues within 4Å:- Chain A: G.148, P.149, R.152, K.158
- Chain B: K.362
Ligand excluded by PLIPACT.4: 2 residues within 4Å:- Chain A: Y.109, D.110
Ligand excluded by PLIPACT.5: 5 residues within 4Å:- Chain A: E.505, S.506, V.508, E.509, H.510
Ligand excluded by PLIPACT.6: 3 residues within 4Å:- Chain A: Y.271, D.307, G.328
Ligand excluded by PLIPACT.7: 7 residues within 4Å:- Chain A: K.44, R.46, R.52, R.496, A.498
- Chain B: T.507
- Ligands: PO4.9
Ligand excluded by PLIPACT.20: 4 residues within 4Å:- Chain B: P.311, H.370, F.372, G.373
Ligand excluded by PLIPACT.21: 3 residues within 4Å:- Chain B: K.258, E.259, G.261
Ligand excluded by PLIPACT.22: 5 residues within 4Å:- Chain B: E.505, S.506, V.508, E.509, H.510
Ligand excluded by PLIPACT.23: 2 residues within 4Å:- Chain B: Y.109, D.110
Ligand excluded by PLIPACT.32: 3 residues within 4Å:- Chain C: K.258, E.259, G.261
Ligand excluded by PLIPACT.33: 5 residues within 4Å:- Chain C: G.148, P.149, R.152, K.158
- Chain D: K.362
Ligand excluded by PLIPACT.34: 2 residues within 4Å:- Chain C: Y.109, D.110
Ligand excluded by PLIPACT.35: 5 residues within 4Å:- Chain C: E.505, S.506, V.508, E.509, H.510
Ligand excluded by PLIPACT.36: 3 residues within 4Å:- Chain C: Y.271, D.307, G.328
Ligand excluded by PLIPACT.37: 7 residues within 4Å:- Chain C: K.44, R.46, R.52, R.496, A.498
- Chain D: T.507
- Ligands: PO4.39
Ligand excluded by PLIPACT.50: 4 residues within 4Å:- Chain D: P.311, H.370, F.372, G.373
Ligand excluded by PLIPACT.51: 3 residues within 4Å:- Chain D: K.258, E.259, G.261
Ligand excluded by PLIPACT.52: 5 residues within 4Å:- Chain D: E.505, S.506, V.508, E.509, H.510
Ligand excluded by PLIPACT.53: 2 residues within 4Å:- Chain D: Y.109, D.110
Ligand excluded by PLIP- 10 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.8: 9 residues within 4Å:- Chain A: D.70, M.71, D.72, T.267, N.268, S.269, K.310
- Ligands: MG.10, GOL.14
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:D.70, A:D.70, A:M.71, A:D.72, A:T.267, A:N.268, A:S.269
- Salt bridges: A:K.310
PO4.9: 7 residues within 4Å:- Chain A: R.52, V.53, V.55, Y.489, Y.493, F.495
- Ligands: ACT.7
6 PLIP interactions:5 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:V.53, A:Y.489
- Water bridges: A:Y.493, A:R.496, B:T.507
- Salt bridges: A:R.52
PO4.24: 8 residues within 4Å:- Chain B: D.70, M.71, D.72, T.267, N.268, S.269, K.310
- Ligands: MG.27
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:D.70, B:M.71, B:D.72, B:D.72, B:T.267, B:N.268, B:S.269
- Salt bridges: B:K.310
PO4.25: 6 residues within 4Å:- Chain B: R.52, V.53, V.55, Y.489, Y.493, F.495
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:V.53, B:V.53, B:Y.493
- Salt bridges: B:R.52
PO4.26: 7 residues within 4Å:- Chain B: D.72, Y.78, Y.83, F.175, H.227, K.233, Y.273
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.78, B:Y.83, B:Y.83
PO4.38: 9 residues within 4Å:- Chain C: D.70, M.71, D.72, T.267, N.268, S.269, K.310
- Ligands: MG.40, GOL.44
10 PLIP interactions:10 interactions with chain C- Hydrogen bonds: C:D.70, C:D.70, C:M.71, C:D.72, C:D.72, C:T.267, C:T.267, C:N.268, C:S.269
- Salt bridges: C:K.310
PO4.39: 7 residues within 4Å:- Chain C: R.52, V.53, V.55, Y.489, Y.493, F.495
- Ligands: ACT.37
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:V.53, C:Y.493
- Water bridges: C:Y.493, C:R.496
- Salt bridges: C:R.52
PO4.54: 8 residues within 4Å:- Chain D: D.70, M.71, D.72, T.267, N.268, S.269, K.310
- Ligands: MG.57
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:D.70, D:M.71, D:D.72, D:N.268, D:S.269
- Salt bridges: D:K.310
PO4.55: 6 residues within 4Å:- Chain D: R.52, V.53, V.55, Y.489, Y.493, F.495
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:V.53, D:V.53, D:Y.489
- Salt bridges: D:R.52
PO4.56: 7 residues within 4Å:- Chain D: D.72, Y.78, Y.83, F.175, H.227, K.233, Y.273
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Y.83
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.10: 4 residues within 4Å:- Chain A: D.70, D.72, D.369
- Ligands: PO4.8
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.70, A:D.72, A:D.369, H2O.2
MG.27: 4 residues within 4Å:- Chain B: D.70, D.72, D.369
- Ligands: PO4.24
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.70, B:D.72, B:D.369
MG.40: 4 residues within 4Å:- Chain C: D.70, D.72, D.369
- Ligands: PO4.38
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.70, C:D.72, C:D.369, H2O.10
MG.57: 4 residues within 4Å:- Chain D: D.70, D.72, D.369
- Ligands: PO4.54
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.70, D:D.72, D:D.369
- 22 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 4 residues within 4Å:- Chain A: F.314, F.372, G.383, W.384
Ligand excluded by PLIPGOL.12: 4 residues within 4Å:- Chain A: K.249, R.256, L.487
- Chain B: S.427
Ligand excluded by PLIPGOL.13: 6 residues within 4Å:- Chain A: Y.73, S.80, L.174, P.391, E.392, Q.395
Ligand excluded by PLIPGOL.14: 7 residues within 4Å:- Chain A: D.72, F.175, H.227, K.233, N.268, S.269
- Ligands: PO4.8
Ligand excluded by PLIPGOL.15: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPGOL.16: 1 residues within 4Å:- Ligands: 5WO.1
Ligand excluded by PLIPGOL.17: 2 residues within 4Å:- Chain A: E.238, N.239
Ligand excluded by PLIPGOL.18: 2 residues within 4Å:- Chain A: K.79, E.241
Ligand excluded by PLIPGOL.28: 5 residues within 4Å:- Chain B: I.98, G.99, D.205, M.210
- Chain D: R.94
Ligand excluded by PLIPGOL.29: 4 residues within 4Å:- Chain A: H.499
- Chain B: F.407, M.448, G.462
Ligand excluded by PLIPGOL.30: 6 residues within 4Å:- Chain B: F.314, F.372, L.376, G.383, W.384, T.386
Ligand excluded by PLIPGOL.41: 4 residues within 4Å:- Chain C: F.314, F.372, G.383, W.384
Ligand excluded by PLIPGOL.42: 4 residues within 4Å:- Chain C: K.249, R.256, L.487
- Chain D: S.427
Ligand excluded by PLIPGOL.43: 6 residues within 4Å:- Chain C: Y.73, S.80, L.174, P.391, E.392, Q.395
Ligand excluded by PLIPGOL.44: 7 residues within 4Å:- Chain C: D.72, F.175, H.227, K.233, N.268, S.269
- Ligands: PO4.38
Ligand excluded by PLIPGOL.45: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPGOL.46: 1 residues within 4Å:- Ligands: 5WO.31
Ligand excluded by PLIPGOL.47: 2 residues within 4Å:- Chain C: E.238, N.239
Ligand excluded by PLIPGOL.48: 2 residues within 4Å:- Chain C: K.79, E.241
Ligand excluded by PLIPGOL.58: 5 residues within 4Å:- Chain B: R.94
- Chain D: I.98, G.99, D.205, M.210
Ligand excluded by PLIPGOL.59: 4 residues within 4Å:- Chain C: H.499
- Chain D: F.407, M.448, G.462
Ligand excluded by PLIPGOL.60: 6 residues within 4Å:- Chain D: F.314, F.372, L.376, G.383, W.384, T.386
Ligand excluded by PLIP- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Marton, Z. et al., Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using a Fragment-Based Approach. J.Med.Chem. (2015)
- Release Date
- 2016-01-13
- Peptides
- Cytosolic purine 5'-nucleotidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.90 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x 5WO: ~{N}-(7~{H}-purin-6-yl)-3-(3-pyrrol-1-ylphenyl)benzamide(Non-covalent)
- 20 x ACT: ACETATE ION(Non-functional Binders)
- 10 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 22 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Marton, Z. et al., Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using a Fragment-Based Approach. J.Med.Chem. (2015)
- Release Date
- 2016-01-13
- Peptides
- Cytosolic purine 5'-nucleotidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B