SMTL ID : 5cr7.1

Human cytosolic 5'-nucleotidase II in complex with N-(9H-Purin-6-yl)-3-(3-pyrrol-1-ylphenyl)benzamide

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)

5WO.1: 9 residues within 4Å: Chain A: L.75, V.77, V.245, D.247, K.249, A.481, S.482, I.484 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.482 Water bridges: A:V.245, A:S.482 5WO.19: 5 residues within 4Å: Chain B: L.75, V.77, V.245, S.482, I.484 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.482 Water bridges: B:L.75, B:V.245 5WO.31: 9 residues within 4Å: Chain C: L.75, V.77, V.245, D.247, K.249, A.481, S.482, I.484 Ligands: GOL.46 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.482 Water bridges: C:V.245, C:S.482 5WO.49: 5 residues within 4Å: Chain D: L.75, V.77, V.245, S.482, I.484 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.482 Water bridges: D:L.75, D:V.245

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 PLIP ACT.3: 5 residues within 4Å: Chain A: G.148, P.149, R.152, K.158 Chain B: K.362 Ligand excluded by PLIP ACT.4: 2 residues within 4Å: Chain A: Y.109, D.110 Ligand excluded by PLIP ACT.5: 5 residues within 4Å: Chain A: E.505, S.506, V.508, E.509, H.510 Ligand excluded by PLIP ACT.6: 3 residues within 4Å: Chain A: Y.271, D.307, G.328 Ligand excluded by PLIP ACT.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 PLIP ACT.20: 4 residues within 4Å: Chain B: P.311, H.370, F.372, G.373 Ligand excluded by PLIP ACT.21: 3 residues within 4Å: Chain B: K.258, E.259, G.261 Ligand excluded by PLIP ACT.22: 5 residues within 4Å: Chain B: E.505, S.506, V.508, E.509, H.510 Ligand excluded by PLIP ACT.23: 2 residues within 4Å: Chain B: Y.109, D.110 Ligand excluded by PLIP ACT.32: 3 residues within 4Å: Chain C: K.258, E.259, G.261 Ligand excluded by PLIP ACT.33: 5 residues within 4Å: Chain C: G.148, P.149, R.152, K.158 Chain D: K.362 Ligand excluded by PLIP ACT.34: 2 residues within 4Å: Chain C: Y.109, D.110 Ligand excluded by PLIP ACT.35: 5 residues within 4Å: Chain C: E.505, S.506, V.508, E.509, H.510 Ligand excluded by PLIP ACT.36: 3 residues within 4Å: Chain C: Y.271, D.307, G.328 Ligand excluded by PLIP ACT.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 PLIP ACT.50: 4 residues within 4Å: Chain D: P.311, H.370, F.372, G.373 Ligand excluded by PLIP ACT.51: 3 residues within 4Å: Chain D: K.258, E.259, G.261 Ligand excluded by PLIP ACT.52: 5 residues within 4Å: Chain D: E.505, S.506, V.508, E.509, H.510 Ligand excluded by PLIP ACT.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 PLIP GOL.12: 4 residues within 4Å: Chain A: K.249, R.256, L.487 Chain B: S.427 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: Y.73, S.80, L.174, P.391, E.392, Q.395 Ligand excluded by PLIP GOL.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 PLIP GOL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.16: 1 residues within 4Å: Ligands: 5WO.1 Ligand excluded by PLIP GOL.17: 2 residues within 4Å: Chain A: E.238, N.239 Ligand excluded by PLIP GOL.18: 2 residues within 4Å: Chain A: K.79, E.241 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: I.98, G.99, D.205, M.210 Chain D: R.94 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain A: H.499 Chain B: F.407, M.448, G.462 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain B: F.314, F.372, L.376, G.383, W.384, T.386 Ligand excluded by PLIP GOL.41: 4 residues within 4Å: Chain C: F.314, F.372, G.383, W.384 Ligand excluded by PLIP GOL.42: 4 residues within 4Å: Chain C: K.249, R.256, L.487 Chain D: S.427 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain C: Y.73, S.80, L.174, P.391, E.392, Q.395 Ligand excluded by PLIP GOL.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 PLIP GOL.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.46: 1 residues within 4Å: Ligands: 5WO.31 Ligand excluded by PLIP GOL.47: 2 residues within 4Å: Chain C: E.238, N.239 Ligand excluded by PLIP GOL.48: 2 residues within 4Å: Chain C: K.79, E.241 Ligand excluded by PLIP GOL.58: 5 residues within 4Å: Chain B: R.94 Chain D: I.98, G.99, D.205, M.210 Ligand excluded by PLIP GOL.59: 4 residues within 4Å: Chain C: H.499 Chain D: F.407, M.448, G.462 Ligand excluded by PLIP GOL.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
A

B
B

C
A

D
B

Cytosolic purine 5'-nucleotidase