SMTL ID : 4mwo.1

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor CPB-T

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x 2E2: 1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

2E2.1: 15 residues within 4Å: Chain A: D.17, F.23, F.49, W.50, V.51, S.52, W.70, S.105, P.106, R.137, R.151 Ligands: PO4.2, K.4, GOL.6, GOL.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.50, A:W.50 Hydrogen bonds: A:V.51, A:S.52, A:S.52, A:S.52, A:P.106 Water bridges: A:T.104, A:S.105, A:I.107, A:K.117, A:K.117 Salt bridges: A:R.137 pi-Stacking: A:W.50 2E2.8: 15 residues within 4Å: Chain B: D.17, F.23, F.49, W.50, V.51, S.52, W.70, S.105, P.106, R.137, R.151 Ligands: PO4.9, K.11, GOL.13, GOL.14 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.50, B:W.50 Hydrogen bonds: B:D.17, B:V.51, B:S.52, B:S.52, B:S.52, B:P.106 Water bridges: B:S.105, B:I.107, B:K.117, B:K.117, B:K.117 Salt bridges: B:R.137 pi-Stacking: B:W.50

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

PO4.2: 9 residues within 4Å: Chain A: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: 2E2.1, K.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:M.16, A:D.17, A:T.104, A:T.104, A:S.105 Water bridges: A:D.15, A:D.17, A:K.117, A:K.139, A:K.139, A:D.149 Salt bridges: A:K.117, A:K.139 PO4.9: 9 residues within 4Å: Chain B: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: 2E2.8, K.11 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:M.16, B:D.17, B:D.17, B:T.104, B:S.105 Water bridges: B:D.15, B:D.17, B:K.117, B:K.139, B:K.139, B:D.149 Salt bridges: B:K.117, B:K.139

4 x K: POTASSIUM ION(Non-covalent)

K.3: 3 residues within 4Å: Chain A: A.93, L.95, T.98 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.93, A:L.95, A:T.98, H2O.6, H2O.6 K.4: 6 residues within 4Å: Chain A: D.15, D.17, D.150 Ligands: 2E2.1, PO4.2, GOL.6 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.7 K.10: 3 residues within 4Å: Chain B: A.93, L.95, T.98 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.93, B:L.95, B:T.98, H2O.15, H2O.15 K.11: 6 residues within 4Å: Chain B: D.15, D.17, D.150 Ligands: 2E2.8, PO4.9, GOL.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.10, H2O.16

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 11 residues within 4Å: Chain A: D.17, G.18, F.23, E.24, R.46, F.49, V.51, D.150, H.172 Ligands: 2E2.1, K.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.46, A:F.49, A:H.172 Water bridges: A:D.150 GOL.7: 7 residues within 4Å: Chain A: W.50, R.137, D.138, R.151, T.155, G.156 Ligands: 2E2.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.137, A:R.137, A:R.151, A:R.151 Water bridges: A:T.140, A:T.155 GOL.12: 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.13: 11 residues within 4Å: Chain B: D.17, G.18, F.23, E.24, R.46, F.49, V.51, D.150, H.172 Ligands: 2E2.8, K.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.24, B:R.46, B:F.49, B:H.172 GOL.14: 7 residues within 4Å: Chain B: W.50, R.137, D.138, R.151, T.155, G.156 Ligands: 2E2.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.137, B:R.137, B:R.151, B:R.151, B:T.155 Water bridges: B:T.140, B:T.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simak, O. et al., Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases. Org.Biomol.Chem. (2014)

Release Date

2014-09-10

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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