SMTL ID : 5cqz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: E.397, W.401, Y.453, S.458, F.460, R.461 Chain B: H.505, E.506 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.397, A:E.397, A:Y.453, A:S.458, B:H.505, B:E.506 GOL.2: 8 residues within 4Å: Chain A: K.45, Y.494, L.495, R.497 Chain B: D.415, L.418, A.419, Y.422 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.415, A:K.45, A:K.45, A:Y.494, A:R.497 GOL.13: 8 residues within 4Å: Chain A: H.505, E.506 Chain B: E.397, W.401, Y.453, S.458, F.460, R.461 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.397, B:Y.453, B:S.458, B:R.461, A:H.505 GOL.14: 8 residues within 4Å: Chain A: D.415, L.418, A.419, Y.422 Chain B: K.45, Y.494, L.495, R.497 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.45, B:K.45, B:L.495, A:D.415 GOL.22: 8 residues within 4Å: Chain C: E.397, W.401, Y.453, S.458, F.460, R.461 Chain D: H.505, E.506 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:H.505, C:E.397, C:S.458 GOL.23: 8 residues within 4Å: Chain C: K.45, Y.494, L.495, R.497 Chain D: D.415, L.418, A.419, Y.422 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:D.415, C:K.45, C:K.45, C:R.497 GOL.34: 8 residues within 4Å: Chain C: H.505, E.506 Chain D: E.397, W.401, Y.453, S.458, F.460, R.461 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.453, D:Y.453, D:S.458, D:R.461, C:H.505, C:E.506 GOL.35: 8 residues within 4Å: Chain C: D.415, L.418, A.419, Y.422 Chain D: K.45, Y.494, L.495, R.497 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.45, D:K.45, D:Y.494, D:L.495, C:D.415

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

SO4.3: 8 residues within 4Å: Chain A: D.71, M.72, D.73, T.268, N.269, S.270, K.311 Ligands: MG.10 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: G.149, P.150, R.153, K.159 Chain B: K.363 Ligand excluded by PLIP SO4.5: 7 residues within 4Å: Chain A: T.116, E.393, Q.396, E.397, Y.453, G.457, L.459 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: V.320, L.321, T.335, T.337 Chain C: F.210, S.212 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: D.271, D.308, G.329, L.331 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: T.166, E.167, Y.170, R.214, F.217, Q.218 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: L.502, E.506, S.507, V.509 Chain B: W.401 Ligand excluded by PLIP SO4.15: 8 residues within 4Å: Chain B: D.71, M.72, D.73, T.268, N.269, S.270, K.311 Ligands: MG.19 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain A: K.363 Chain B: G.149, P.150, R.153, K.159 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain B: F.176, R.221, V.224, D.225, H.228 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: L.502, E.506, S.507, V.509 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain C: D.71, M.72, D.73, T.268, N.269, S.270, K.311 Ligands: MG.31 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain C: G.149, P.150, R.153, K.159 Chain D: K.363 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain C: T.116, E.393, Q.396, E.397, Y.453, G.457, L.459 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain A: F.210, S.212 Chain C: V.320, L.321, T.335, T.337 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: D.271, D.308, G.329, L.331 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain C: T.166, E.167, Y.170, R.214, F.217, Q.218 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain C: L.502, E.506, S.507, V.509 Chain D: W.401 Ligand excluded by PLIP SO4.36: 8 residues within 4Å: Chain D: D.71, M.72, D.73, T.268, N.269, S.270, K.311 Ligands: MG.40 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain C: K.363 Chain D: G.149, P.150, R.153, K.159 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain D: F.176, R.221, V.224, D.225, H.228 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain D: L.502, E.506, S.507, V.509 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.10: 4 residues within 4Å: Chain A: D.71, D.73, D.370 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.71, A:D.71, A:D.73, A:D.370 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain B: D.71, D.73, D.370 Ligands: SO4.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.71, B:D.71, B:D.73, B:D.370, H2O.2 MG.20: 4 residues within 4Å: Chain B: R.58, T.387, Y.476, D.478 No protein-ligand interaction detected (PLIP) MG.31: 4 residues within 4Å: Chain C: D.71, D.73, D.370 Ligands: SO4.24 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.71, C:D.71, C:D.73, C:D.370 MG.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 4 residues within 4Å: Chain D: D.71, D.73, D.370 Ligands: SO4.36 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.71, D:D.71, D:D.73, D:D.370, H2O.5 MG.41: 4 residues within 4Å: Chain D: R.58, T.387, Y.476, D.478 No protein-ligand interaction detected (PLIP)

4 x 53O: 1-(biphenyl-3-yl)-1H-imidazole(Non-covalent)

53O.12: 6 residues within 4Å: Chain A: S.59, L.495, R.497 Chain B: Q.439, S.464, R.465 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.465 53O.21: 6 residues within 4Å: Chain A: Q.439, S.464, R.465 Chain B: R.58, S.59, R.497 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:R.58, A:R.465 53O.33: 6 residues within 4Å: Chain C: S.59, L.495, R.497 Chain D: Q.439, S.464, R.465 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:R.465 53O.42: 6 residues within 4Å: Chain C: Q.439, S.464, R.465 Chain D: R.58, S.59, R.497 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:R.465, D:R.58

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

2015-12-23

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

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