SMTL ID : 6g2m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

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

BME.1: 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.9: 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: P.39, F.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.40 Water bridges: A:F.40, A:D.45 GOL.3: 7 residues within 4Å: Chain A: G.84, E.87, A.88, W.188, A.189, D.190, W.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.91, A:A.189 Water bridges: A:W.192 GOL.4: 3 residues within 4Å: Chain A: N.74, F.77, Y.115 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:K.111, A:E.116 Hydrogen bonds: A:N.74 GOL.10: 2 residues within 4Å: Chain B: P.39, F.40 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.40 Water bridges: B:F.40, B:D.45 GOL.11: 7 residues within 4Å: Chain B: G.84, E.87, A.88, W.188, A.189, D.190, W.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.189 Water bridges: B:W.192 GOL.12: 3 residues within 4Å: Chain B: N.74, F.77, Y.115 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.74, B:Y.115 Water bridges: A:K.111

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)

O84.5: 15 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, R.137, K.139 Ligands: MG.7 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:D.17, A:F.49, A:W.50, A:W.70, A:I.107 Hydrogen bonds: A:D.17, A:F.49, A:V.51, A:S.105, A:S.105, A:K.108, A:R.137, A:R.137, A:K.139 Water bridges: A:M.16, A:D.17, A:E.24, A:R.46, A:S.52, A:K.108, A:M.109 pi-Stacking: A:F.23, A:W.50 pi-Cation interactions: A:R.137 O84.13: 15 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, R.137, K.139 Ligands: MG.15 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:D.17, B:F.49, B:W.50, B:W.70, B:I.107 Hydrogen bonds: B:D.17, B:F.49, B:V.51, B:S.105, B:S.105, B:K.108, B:R.137, B:R.137, B:K.139 Water bridges: B:M.16, B:R.46, B:S.52, B:T.104, B:K.108, B:M.109 pi-Stacking: B:F.23, B:W.50 pi-Cation interactions: B:R.137

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

EDO.6: 7 residues within 4Å: Chain A: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.99, A:V.100 EDO.14: 7 residues within 4Å: Chain B: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.1, B:D.99, B:D.99, B:V.100

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain A: D.15, D.17, D.149, D.150 Ligands: O84.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.15, A:D.17, A:D.150, H2O.1, H2O.3 MG.15: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: O84.13 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.14

2 x K: POTASSIUM ION(Non-covalent)

K.8: 4 residues within 4Å: Chain A: P.152, I.154, H.165, R.182 No protein-ligand interaction detected (PLIP) K.16: 4 residues within 4Å: Chain B: P.152, I.154, H.165, R.182 No protein-ligand interaction detected (PLIP)

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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