SMTL ID : 7zeh.3 (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

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

IPQ.1: 11 residues within 4Å: Chain A: Y.62, D.66, L.79, L.83, W.107, W.108, A.111, H.112, L.115 Ligands: RBL.2, EDO.6 9 PLIP interactions: 9 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

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

RBL.2: 6 residues within 4Å: Chain A: Y.87, E.90, W.108, T.204 Ligands: IPQ.1, PO4.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.90 Water bridges: A:T.204, A:T.204, A:S.233

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

EDO.3: 6 residues within 4Å: Chain A: Q.39, I.41, F.155, F.157, S.209, V.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.39, A:S.209 EDO.4: 4 residues within 4Å: Chain A: A.52, G.55, K.56, R.57 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.55 EDO.5: 5 residues within 4Å: Chain A: N.63, D.66, N.67, R.76 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.63, A:D.66 Water bridges: A:T.80, A:T.80 EDO.6: 6 residues within 4Å: Chain A: D.66, L.79, T.80, L.83 Ligands: IPQ.1, EDO.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.66, A:D.66, A:T.80 Water bridges: A:T.80, A:T.80 EDO.7: 4 residues within 4Å: Chain A: L.83, H.84, Y.87, P.88 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: R.95, H.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.95, A:R.95 EDO.9: 6 residues within 4Å: Chain A: V.129, R.130, S.132, A.134, Q.171, M.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.132, A:Q.171 EDO.10: 4 residues within 4Å: Chain A: M.135, L.136, Y.140, M.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.136, A:L.136 EDO.11: 3 residues within 4Å: Chain A: T.146, H.149, N.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.149, A:N.150 EDO.12: 2 residues within 4Å: Chain A: K.198, G.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.199 Water bridges: A:D.187, A:F.197

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 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.3

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

PO4.14: 6 residues within 4Å: Chain A: Y.62, S.158, A.159, T.204, K.207 Ligands: RBL.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.62, A:A.159, A:T.204 Water bridges: A:D.43, A:F.44, A:D.45, 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)

SO4.15: 4 residues within 4Å: Chain A: S.233, I.234, G.235, Y.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.233, A:I.234, A:G.235 Water bridges: A:S.233

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
C

7-methylguanosine phosphate-specific 5'-nucleotidase

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