SMTL ID : 4yik.1

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

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: 2O2.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.15, A:D.17, A:D.150, H2O.2, H2O.3 MG.14: 5 residues within 4Å: Chain B: D.15, D.17, D.149, D.150 Ligands: 2O2.19 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.2, A:N.2, A:V.100 Water bridges: A:N.2, A:N.2, A:Q.132, A:Q.132 GOL.3: 8 residues within 4Å: Chain A: G.84, E.87, A.88, E.91, 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: 4 residues within 4Å: Chain A: W.50, R.151, P.152, D.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.151, A:D.153, A:D.153, A:D.153 GOL.5: 4 residues within 4Å: Chain A: R.11, A.144, D.145, S.162 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.11, A:D.145 Water bridges: A:R.8, A:R.8, A:S.162, A:S.162 GOL.15: 7 residues within 4Å: Chain B: S.1, N.2, A.93, T.98, D.99, V.100, Q.132 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.1, B:N.2, B:N.2, B:D.99, B:V.100 Water bridges: B:N.2, B:N.2, B:Q.132, B:Q.132 GOL.16: 8 residues within 4Å: Chain B: G.84, E.87, A.88, E.91, 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.17: 4 residues within 4Å: Chain B: W.50, R.151, P.152, D.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.151, B:D.153, B:D.153 GOL.18: 4 residues within 4Å: Chain B: R.11, A.144, D.145, S.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.11, B:D.145 Water bridges: B:R.8, B:R.8, B:S.162, B:S.162

2 x 2O2: 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

2O2.6: 13 residues within 4Å: Chain A: D.15, D.17, F.23, F.49, W.50, V.51, W.70, S.105, I.107, K.108, R.137 Ligands: MG.1, TRS.7 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.23, A:F.49, A:F.49, A:W.50, A:W.70 Hydrogen bonds: A:D.17, A:D.17, A:D.17, A:F.49, A:V.51, A:S.105, A:K.108, A:R.137, A:R.137 Water bridges: A:E.24, A:S.52, A:M.109, A:K.117, A:K.139 pi-Stacking: A:W.50 pi-Cation interactions: A:R.137 2O2.19: 13 residues within 4Å: Chain B: D.15, D.17, F.23, F.49, W.50, V.51, W.70, S.105, I.107, K.108, R.137 Ligands: MG.14, TRS.20 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.23, B:F.49, B:F.49, B:W.50, B:W.70 Hydrogen bonds: B:D.17, B:D.17, B:F.49, B:V.51, B:S.105, B:K.108, B:R.137, B:R.137 Water bridges: B:S.52, B:T.104, B:M.109, B:K.139 pi-Stacking: B:W.50 pi-Cation interactions: B:R.137

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

TRS.7: 8 residues within 4Å: Chain A: D.17, F.23, F.49, W.50, F.76, S.105, I.107 Ligands: 2O2.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.17 Water bridges: A:D.17 TRS.20: 8 residues within 4Å: Chain B: D.17, F.23, F.49, W.50, F.76, S.105, I.107 Ligands: 2O2.19 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.17

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

PEG.8: 8 residues within 4Å: Chain A: R.46, R.47, C.171, H.172, N.173, Q.174, H.175, L.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.47, A:C.171, A:H.175, A:L.176 Water bridges: A:R.46 PEG.9: 3 residues within 4Å: Chain A: R.184, H.186, D.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.190 PEG.10: 8 residues within 4Å: Chain A: A.157, P.159 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 Hydrogen bonds: B:N.2, B:A.3, B:A.9 Water bridges: B:R.11, A:A.157 PEG.11: 3 residues within 4Å: Chain A: P.181, R.182, R.183 No protein-ligand interaction detected (PLIP) PEG.12: 3 residues within 4Å: Chain A: F.77, E.78, K.123 No protein-ligand interaction detected (PLIP) PEG.21: 8 residues within 4Å: Chain B: R.46, R.47, C.171, H.172, N.173, Q.174, H.175, L.176 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.47, B:C.171, B:H.175, B:L.176 Water bridges: B:R.46 PEG.22: 3 residues within 4Å: Chain B: R.184, H.186, D.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.190 PEG.23: 8 residues within 4Å: Chain A: N.2, A.3, G.7, R.8, A.9, D.99 Chain B: A.157, P.159 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.2, A:A.3, A:A.9 Water bridges: A:A.9, A:D.99 PEG.24: 3 residues within 4Å: Chain B: P.181, R.182, R.183 No protein-ligand interaction detected (PLIP) PEG.25: 3 residues within 4Å: Chain B: F.77, E.78, K.123 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.78

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

PO4.13: 6 residues within 4Å: Chain A: P.152, D.153, I.154, W.163, H.165, R.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.152, A:I.154 Salt bridges: A:H.165, A:R.182 PO4.26: 6 residues within 4Å: Chain B: P.152, D.153, I.154, W.163, H.165, R.182 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.152, B:I.154 Salt bridges: B:H.165, B:R.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pachl, P. et al., Structure-based design of a bisphosphonate 5'(3')-deoxyribonucleotidase inhibitor. Medchemcomm (2015)

Release Date

2015-09-09

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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