SMTL ID : 3rsr.1

Crystal Structure of 5-NITP Inhibition of Yeast Ribonucleotide Reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 1 residues within 4Å: Ligands: N5P.2 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: N5P.4 No protein-ligand interaction detected (PLIP)

2 x N5P: 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE(Non-covalent)

N5P.2: 15 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, I.255, R.256, I.262, A.263, G.264, T.265, S.269 Chain B: K.243, Y.285, V.286 Ligands: MG.1 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.228, A:I.228, A:I.231, A:I.262, B:V.286 Hydrogen bonds: A:D.226, A:I.228, A:A.263, A:G.264, A:T.265, B:K.243 Water bridges: A:S.227, A:E.229, A:R.256, A:R.256, A:R.256, A:R.256 Salt bridges: A:R.256, B:K.243, B:K.243 N5P.4: 15 residues within 4Å: Chain A: K.243, Y.285, V.286 Chain B: D.226, S.227, I.228, I.231, I.255, R.256, I.262, A.263, G.264, T.265, S.269 Ligands: MG.3 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.228, B:I.228, B:I.231, B:I.262, A:V.286 Hydrogen bonds: B:D.226, B:I.228, B:A.263, B:G.264, B:T.265, A:K.243 Water bridges: B:E.229, B:R.256, B:R.256, B:R.256, B:R.256, A:K.243 Salt bridges: B:R.256, A:K.243, A:K.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M.F. et al., Evaluating the therapeutic potential of a non-natural nucleotide that inhibits human ribonucleotide reductase. Mol.Cancer Ther. (2012)

Release Date

2012-11-14

Peptides

Ribonucleoside-diphosphate reductase large chain 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribonucleoside-diphosphate reductase large chain 1

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