SMTL ID : 6g22.1

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PEU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.15, D.17, D.150 Ligands: 2O2.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.15, A:D.17, A:D.150, H2O.2, H2O.2 MG.6: 4 residues within 4Å: Chain B: D.15, D.17, D.150 Ligands: 2O2.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.15, B:D.17, B:D.150, H2O.11, H2O.11

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 4 residues within 4Å: Chain A: T.169, A.170, C.171, Q.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.169 BME.7: 4 residues within 4Å: Chain B: T.169, A.170, C.171, Q.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.169

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.49, W.50, R.151, P.152, D.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.50, A:R.151, A:D.153, A:D.153, A:D.153 GOL.4: 7 residues within 4Å: Chain A: A.93, S.94, L.95, Q.96, N.97, T.98, D.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.93, A:T.98, A:D.99 Water bridges: A:N.97 GOL.8: 5 residues within 4Å: Chain B: F.49, W.50, R.151, P.152, D.153 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.50, B:R.151, B:D.153, B:D.153 GOL.9: 7 residues within 4Å: Chain B: A.93, S.94, L.95, Q.96, N.97, T.98, D.99 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.93, B:T.98, B:D.99 Water bridges: B:N.97, B:D.99, B:D.99

2 x 2O2: 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

2O2.5: 12 residues within 4Å: Chain A: D.15, D.17, F.23, F.49, W.50, V.51, W.70, S.105, I.107, K.108, R.137 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.50, A:W.70, A:I.107 Hydrogen bonds: A:D.17, A:F.49, A:V.51, A:S.105, A:K.108, A:R.137, A:R.137 Water bridges: A:D.15, A:S.52, A:M.109, A:K.117, A:K.117, A:K.139, A:D.149 pi-Stacking: A:F.23, A:W.50 pi-Cation interactions: A:R.137 2O2.10: 12 residues within 4Å: Chain B: D.15, D.17, F.23, F.49, W.50, V.51, W.70, S.105, I.107, K.108, R.137 Ligands: MG.6 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.50, B:W.70, B:I.107 Hydrogen bonds: B:F.49, B:V.51, B:S.105, B:K.108, B:R.137, B:R.137 Water bridges: B:D.15, B:S.52, B:T.104, B:M.109, B:K.117, B:K.139, B:D.149 pi-Stacking: B:F.23, B:W.50 pi-Cation interactions: B:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pachl, P. et al., Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases. Eur.J.Org.Chem. (2018)

Release Date

2018-07-11

Peptides

5'(3')-deoxyribonucleotidase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5'(3')-deoxyribonucleotidase, mitochondrial

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