SMTL ID : 4p5e.2 (1 other biounit)

CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x N6P: 6-(naphthalen-2-yl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine(Non-covalent)

N6P.1: 20 residues within 4Å: Chain A: Y.6, C.8, G.9, S.10, I.11, R.12, G.13, H.38, V.39, G.48, E.49, I.58, D.62, S.80, L.81, G.82, V.83, E.86 Chain B: S.110, M.112 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.49, A:I.58 Hydrogen bonds: A:G.9, A:S.10, A:I.11, A:R.12, A:G.13, A:D.62, A:S.80, A:S.80, A:G.82, A:V.83 Water bridges: A:L.81, A:L.81 N6P.2: 18 residues within 4Å: Chain A: S.110, A.111, M.112 Chain B: Y.6, C.8, G.9, S.10, I.11, R.12, G.13, V.39, I.58, D.62, S.80, L.81, G.82, V.83, E.86 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.58 Hydrogen bonds: B:G.9, B:I.11, B:R.12, B:G.13, B:D.62, B:S.80, B:S.80, B:L.81, B:G.82, B:V.83, A:S.110

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain B: D.143, P.144, E.146 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.143, B:P.144, B:E.146, H2O.9, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amiable, C. et al., 6-(Hetero)Arylpurine nucleotides as inhibitors of the oncogenic target DNPH1: Synthesis, structural studies and cytotoxic activities. Eur.J.Med.Chem. (2014)

Release Date

2014-08-20

Peptides

2'-deoxynucleoside 5'-phosphate N-hydrolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-deoxynucleoside 5'-phosphate N-hydrolase 1

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