SMTL ID : 6g2l.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.15, D.17, D.149, D.150 Ligands: EJ8.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.15, A:D.17, A:D.150, H2O.1, H2O.2 MG.6: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: EJ8.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.15, B:D.17, B:D.150, H2O.12, H2O.13

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 Water bridges: 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 Water bridges: B:T.169

2 x EJ8: [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)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)

EJ8.3: 16 residues within 4Å: Chain A: D.15, D.17, F.23, F.49, W.50, V.51, W.70, T.104, S.105, P.106, I.107, K.108, K.117, R.137, K.139 Ligands: MG.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.50, A:W.70, A:I.107 Hydrogen bonds: A:D.15, A:D.17, A:D.17, A:F.49, A:V.51, A:S.105, A:K.108, A:K.117, A:R.137, A:R.137, A:K.139, A:K.139 Water bridges: A:E.24, A:R.46, A:S.52, A:W.70, A:M.109 pi-Stacking: A:F.23 pi-Cation interactions: A:R.137 EJ8.8: 16 residues within 4Å: Chain B: D.15, D.17, F.23, F.49, W.50, V.51, W.70, T.104, S.105, P.106, I.107, K.108, K.117, R.137, K.139 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.50, B:W.70, B:I.107 Hydrogen bonds: B:D.15, B:D.17, B:F.49, B:V.51, B:T.104, B:S.105, B:K.108, B:K.117, B:R.137, B:R.137, B:K.139, B:K.139 Water bridges: B:R.46, B:S.52, B:W.70, B:M.109 pi-Stacking: B:F.23 pi-Cation interactions: B:R.137

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.2, A:N.2, A:V.100, A:V.100 Water bridges: A:Q.132, A:Q.132 GOL.5: 5 residues within 4Å: Chain A: R.8, R.11, A.144, D.145, S.162 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.11 Water bridges: A:D.145, A:D.145, A:D.145, A:D.145, A:S.162 GOL.9: 7 residues within 4Å: Chain B: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.1, B:N.2, B:N.2, B:D.99, B:V.100, B:V.100 Water bridges: B:Q.132, B:Q.132 GOL.10: 5 residues within 4Å: Chain B: R.8, R.11, A.144, D.145, S.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.11 Water bridges: B:D.145, B:D.145, B:D.145, B:D.145, B:S.162

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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