SMTL ID : 7zeh.4 (3 other biounits)

Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7Guanine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: F.188, N.189, G.192 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: F.155, H.180, I.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.181 EDO.5: 5 residues within 4Å: Chain A: F.51, A.52, G.55, K.56, R.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.55 Water bridges: A:G.55 EDO.6: 4 residues within 4Å: Chain A: R.57, C.58, S.60, N.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.60, A:N.63 Water bridges: A:R.57 EDO.7: 4 residues within 4Å: Chain A: N.63, D.66, N.67, R.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.62, A:N.63 EDO.8: 5 residues within 4Å: Chain A: R.170, K.173, V.174, F.175, H.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:F.175 Water bridges: A:H.176 EDO.9: 2 residues within 4Å: Chain A: K.198, G.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.199 Water bridges: A:F.197 EDO.10: 5 residues within 4Å: Chain A: H.112, N.113, C.116, G.196, F.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.112, A:F.197, A:F.197

1 x IPQ: N7-(3,4-difluorobenzyl) guanine(Non-covalent)

IPQ.2: 10 residues within 4Å: Chain A: Y.62, L.65, D.66, L.79, W.107, W.108, A.111, H.112, L.115 Ligands: RBL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.107, A:W.107, A:W.108, A:W.108 Hydrogen bonds: A:Y.62, A:H.112 Salt bridges: A:D.66 pi-Stacking: A:Y.62, A:Y.62, A:Y.62, A:W.108

1 x RBL: D-ribulose(Post Translational Modification)

RBL.3: 6 residues within 4Å: Chain A: Y.87, E.90, W.108, T.204 Ligands: IPQ.2, PO4.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.90 Hydrogen bonds: A:T.204 Water bridges: A:T.204, A:T.204, A:S.233, A:S.233

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 3 residues within 4Å: Chain A: D.43, D.45, D.232 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.43, A:D.45, A:D.232, H2O.2, H2O.2, H2O.2

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 7 residues within 4Å: Chain A: D.43, Y.62, S.158, A.159, T.204, K.207 Ligands: RBL.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.62, A:A.159 Water bridges: A:D.43, A:F.44, A:D.45, A:D.45, A:K.207, A:K.207 Salt bridges: A:K.207

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

SO4.13: 5 residues within 4Å: Chain A: S.233, I.234, G.235, R.262, Y.266 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.234, A:G.235, A:Y.266 Water bridges: A:S.233 Salt bridges: A:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubacka, D. et al., Substrate-Based Design of Cytosolic Nucleotidase IIIB Inhibitors and Structural Insights into Inhibition Mechanism. Pharmaceuticals (2022)

Release Date

2022-05-25

Peptides

7-methylguanosine phosphate-specific 5'-nucleotidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

7-methylguanosine phosphate-specific 5'-nucleotidase

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