SMTL ID : 6g2n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.14, D.16, D.148, D.149 Ligands: O84.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:D.16, A:D.149, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain B: D.14, D.16, D.148, D.149 Ligands: O84.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.14, B:D.16, B:D.149, H2O.7, H2O.7

2 x O84: [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid(Non-covalent)

O84.2: 15 residues within 4Å: Chain A: D.14, D.16, F.22, F.48, L.49, A.50, Y.69, T.103, S.104, P.105, L.106, L.107, R.136, K.138 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:D.16, A:F.48, A:Y.69, A:L.106 Hydrogen bonds: A:D.16, A:F.48, A:A.50, A:S.104, A:S.104, A:L.107, A:R.136, A:R.136, A:K.138 Water bridges: A:M.15, A:R.45, A:R.51, A:T.103, A:K.108 pi-Stacking: A:F.22 pi-Cation interactions: A:R.136 O84.4: 15 residues within 4Å: Chain B: D.14, D.16, F.22, F.48, L.49, A.50, Y.69, T.103, S.104, P.105, L.106, L.107, R.136, K.138 Ligands: MG.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:D.16, B:F.48, B:Y.69, B:L.106 Hydrogen bonds: B:D.16, B:F.48, B:A.50, B:S.104, B:L.107, B:R.136, B:R.136, B:K.138 Water bridges: B:M.15, B:R.45, B:R.51, B:T.103, B:K.108 pi-Stacking: B:F.22 pi-Cation interactions: B:R.136

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, cytosolic type: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

5'(3')-deoxyribonucleotidase, cytosolic type