SMTL ID : 4nfl.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 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: PO4.2 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.1 MG.19: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: PO4.20 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.12

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

PO4.2: 11 residues within 4Å: Chain A: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.1, 2JW.3, GOL.10, GOL.11 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.15, A:D.15, A:M.16, A:D.17, A:D.17, A:D.17, A:S.105 Water bridges: A:S.105, A:S.105, A:K.117 Salt bridges: A:K.117, A:K.139 PO4.20: 11 residues within 4Å: Chain B: D.15, M.16, D.17, T.104, S.105, K.117, K.139 Ligands: MG.19, 2JW.21, GOL.28, GOL.29 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.15, B:D.15, B:M.16, B:D.17, B:D.17, B:T.104, B:S.105 Water bridges: B:S.105, B:S.105, B:K.117 Salt bridges: B:K.117, B:K.139

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

2JW.3: 14 residues within 4Å: Chain A: F.23, F.49, W.50, V.51, W.70, S.105, P.106, I.107, K.108, R.137, R.151 Ligands: PO4.2, GOL.10, GOL.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.49, A:W.50, A:W.50, A:W.70, A:I.107 Hydrogen bonds: A:V.51, A:S.105, A:K.108, A:R.137, A:R.137 Water bridges: A:S.52 pi-Stacking: A:F.23, A:W.50 pi-Cation interactions: A:R.137 2JW.21: 14 residues within 4Å: Chain B: F.23, F.49, W.50, V.51, W.70, S.105, P.106, I.107, K.108, R.137, R.151 Ligands: PO4.20, GOL.28, GOL.29 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.49, B:W.50, B:W.50, B:W.70, B:I.107 Hydrogen bonds: B:V.51, B:S.105, B:K.108, B:R.137, B:R.137 Water bridges: B:S.52 pi-Stacking: B:F.23, B:W.50 pi-Cation interactions: B:R.137

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 7 residues within 4Å: Chain A: W.188, A.189, D.190, D.191, W.192, K.193 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.188, A:D.191, A:W.192, A:W.192, A:K.193 TRS.22: 7 residues within 4Å: Chain B: W.188, A.189, D.190, D.191, W.192, K.193 Ligands: GOL.27 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.188, B:W.192, B:W.192, B:K.193

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.22, G.25, G.26, R.29, E.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.22, A:R.29 Water bridges: A:R.29, A:E.80, A:E.80 GOL.6: 7 residues within 4Å: Chain A: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.98, A:V.100 Water bridges: A:N.2, A:N.2 GOL.7: 5 residues within 4Å: Chain A: N.74, F.77, Y.115, E.116 Ligands: PEG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.116, A:E.116 GOL.8: 5 residues within 4Å: Chain A: F.49, W.50, R.151, P.152, D.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.151, A:D.153, A:D.153, A:D.153 Water bridges: A:D.153 GOL.9: 8 residues within 4Å: Chain A: G.84, E.87, A.88, E.91, W.188, A.189, W.192 Ligands: TRS.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.88, A:E.91, A:W.192 GOL.10: 8 residues within 4Å: Chain A: D.17, F.23, E.24, F.49, H.172 Ligands: PO4.2, 2JW.3, GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.24, A:H.172 Water bridges: A:E.24 GOL.11: 9 residues within 4Å: Chain A: D.17, F.49, W.50, S.105, P.106, R.137 Ligands: PO4.2, 2JW.3, GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.17, A:D.17 GOL.23: 5 residues within 4Å: Chain B: D.22, G.25, G.26, R.29, E.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.22, B:D.22, B:R.29 Water bridges: B:R.29, B:E.80 GOL.24: 7 residues within 4Å: Chain B: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.1, B:T.98, B:D.99, B:V.100 Water bridges: B:N.2, B:N.2 GOL.25: 5 residues within 4Å: Chain B: N.74, F.77, Y.115, E.116 Ligands: PEG.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.115, B:E.116 GOL.26: 5 residues within 4Å: Chain B: F.49, W.50, R.151, P.152, D.153 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.151, B:D.153, B:D.153 Water bridges: B:D.153 GOL.27: 8 residues within 4Å: Chain B: G.84, E.87, A.88, E.91, W.188, A.189, W.192 Ligands: TRS.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.88, B:W.192 GOL.28: 8 residues within 4Å: Chain B: D.17, F.23, E.24, F.49, H.172 Ligands: PO4.20, 2JW.21, GOL.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.172 Water bridges: B:E.24, B:D.150 GOL.29: 9 residues within 4Å: Chain B: D.17, F.49, W.50, S.105, P.106, R.137 Ligands: PO4.20, 2JW.21, GOL.28 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.17

14 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.12: 3 residues within 4Å: Chain A: F.77, K.123 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.122, A:E.122, A:E.122, A:E.122 PEG.13: 7 residues within 4Å: Chain A: N.2, A.3, G.7, R.8, A.9, D.99 Chain B: A.157 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.2, A:A.3, A:A.9 Hydrogen bonds: A:A.9, B:A.157 Water bridges: A:D.99 PEG.14: 4 residues within 4Å: Chain A: K.30, K.73, N.74, E.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.30, A:N.74 Water bridges: A:S.72, A:K.73 PEG.15: 9 residues within 4Å: Chain A: R.46, R.47, G.48, C.171, H.172, N.173, Q.174, H.175, L.176 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.47, A:G.48, A:C.171 Water bridges: A:F.49 PEG.16: 5 residues within 4Å: Chain A: P.152, D.153, I.154, H.165, R.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.154, A:H.165 Water bridges: A:D.153 PEG.17: 6 residues within 4Å: Chain A: L.178, Q.179, P.180, R.182, R.183, R.184 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.184 PEG.18: 3 residues within 4Å: Chain A: D.22, G.25, L.43 No protein-ligand interaction detected (PLIP) PEG.30: 3 residues within 4Å: Chain B: F.77, K.123 Ligands: GOL.25 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.122, B:E.122, B:E.122 PEG.31: 7 residues within 4Å: Chain A: A.157 Chain B: N.2, A.3, G.7, R.8, A.9, D.99 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.2, B:A.3, B:A.9 Hydrogen bonds: B:A.9, A:A.157 PEG.32: 4 residues within 4Å: Chain B: K.30, K.73, N.74, E.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.30, B:N.74 Water bridges: B:S.72, B:K.73 PEG.33: 9 residues within 4Å: Chain B: R.46, R.47, G.48, C.171, H.172, N.173, Q.174, H.175, L.176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.47, B:G.48, B:C.171 Water bridges: B:F.49 PEG.34: 5 residues within 4Å: Chain B: P.152, D.153, I.154, H.165, R.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.153, B:I.154, B:H.165 Water bridges: B:D.153 PEG.35: 6 residues within 4Å: Chain B: L.178, Q.179, P.180, R.182, R.183, R.184 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.184 PEG.36: 3 residues within 4Å: Chain B: D.22, G.25, L.43 No protein-ligand interaction detected (PLIP)

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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