SMTL ID : 7zeg.1 (1 other biounit)

Human cytosolic 5' nucleotidase IIIB in complex with 3,4-diF-Bn7GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x IOO: N7-(3,4-difluorobenzyl) guanosine 5'-monophosphate(Non-covalent)

IOO.1: 18 residues within 4Å: Chain A: Y.62, N.63, L.65, D.66, L.83, Y.87, E.90, W.107, W.108, A.111, H.112, L.115, S.158, A.159, G.160, I.161, T.204, K.207 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.111 Hydrogen bonds: A:Y.62, A:N.63, A:E.90, A:A.159, A:G.160 Water bridges: A:D.45, A:D.45, A:S.60, A:N.63, A:N.63, A:T.204, A:K.207, A:K.207, A:K.207 Salt bridges: A:D.66, A:K.207 pi-Stacking: A:Y.62, A:Y.62, A:W.108

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

EDO.2: 1 residues within 4Å: Chain A: Y.87 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: Y.148, H.176, P.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.176

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 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.3, H2O.5

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

2022-04-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

7-methylguanosine phosphate-specific 5'-nucleotidase

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