SMTL ID : 4yih.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.10, D.12, D.145 Ligands: PO4.2, 2O2.3, GOL.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.10, A:D.12, A:D.145, H2O.3 MG.5: 6 residues within 4Å: Chain B: D.10, D.12, D.144, D.145 Ligands: PO4.6, 2O2.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:D.12, B:D.145, H2O.7

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

PO4.2: 9 residues within 4Å: Chain A: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.1, 2O2.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:M.11, A:D.12, A:S.100, A:S.100 Water bridges: A:K.112, A:K.134, A:K.134 Salt bridges: A:K.112, A:K.134 PO4.6: 9 residues within 4Å: Chain B: D.10, M.11, D.12, T.99, S.100, K.112, K.134 Ligands: MG.5, 2O2.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.11, B:D.12, B:D.12, B:D.12, B:D.12, B:S.100 Water bridges: B:K.112 Salt bridges: B:K.112, B:K.134

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)

2O2.3: 15 residues within 4Å: Chain A: D.12, F.18, F.44, L.45, A.46, R.47, Y.65, S.100, P.101, L.102, L.103, R.132 Ligands: MG.1, PO4.2, GOL.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.18, A:F.44 Hydrogen bonds: A:A.46, A:R.47, A:L.103, A:R.132, A:R.132 Water bridges: A:D.12, A:Y.65, A:Y.65, A:K.104, A:K.104, A:K.112, A:K.112 2O2.7: 13 residues within 4Å: Chain B: D.12, F.18, F.44, L.45, A.46, R.47, Y.65, S.100, L.102, L.103, R.132 Ligands: MG.5, PO4.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.18, B:F.44, B:F.44, B:L.102 Hydrogen bonds: B:D.12, B:A.46, B:R.47, B:Y.65, B:L.103, B:R.132, B:R.132 Water bridges: B:L.102, B:K.112

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: D.12, G.13, F.18, E.19, F.44, D.145, C.165, H.167 Ligands: MG.1, 2O2.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.44, A:D.145 Water bridges: A:A.16, A:F.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pachl, P. et al., Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor. Medchemcomm (2015)

Release Date

2015-09-09

Peptides

5'(3')-deoxyribonucleotidase, cytosolic type: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'(3')-deoxyribonucleotidase, cytosolic type

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