SMTL ID : 5tus.3 (2 other biounits)

Potent competitive inhibition of human ribonucleotide reductase by a novel non-nucleoside small molecule

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-dimer

Ligands

2 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.1: 18 residues within 4Å: Chain A: D.226, S.227, I.228, I.231, I.255, R.256, I.262, A.263, G.264, S.269, N.270 Chain B: K.243, Y.285, V.286, D.287, Q.288, G.289 Ligands: MG.2 18 PLIP interactions: 8 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:K.243, A:I.228, A:I.231, A:I.262 Hydrogen bonds: B:Y.285, B:Y.285, B:D.287, B:Q.288, B:G.289, A:D.226, A:I.228, A:A.263, A:G.264, A:N.270, A:N.270 Salt bridges: B:K.243, B:K.243, A:R.256 TTP.3: 18 residues within 4Å: Chain A: K.243, Y.285, V.286, D.287, Q.288, G.289 Chain B: D.226, S.227, I.228, I.231, I.255, R.256, I.262, A.263, G.264, S.269, N.270 Ligands: MG.4 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.228, B:I.228, B:I.231, B:I.262, A:K.243 Hydrogen bonds: B:D.226, B:I.228, B:R.256, B:A.263, B:G.264, B:N.270, B:N.270, A:Y.285, A:D.287 Salt bridges: B:R.256, B:R.256, A:K.243, A:K.243

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

MG.2: 1 residues within 4Å: Ligands: TTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: S.227 Ligands: TTP.3 No protein-ligand interaction detected (PLIP)

1 x 7LL: 2-hydroxy-N'-[(Z)-(2-hydroxynaphthalen-1-yl)methylidene]benzohydrazide(Non-covalent)

7LL.5: 15 residues within 4Å: Chain B: H.200, A.201, S.202, S.217, C.218, G.247, L.428, C.429, L.446, M.602, P.603, T.604, A.605, S.606, T.607 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.201, B:L.428, B:T.607 Hydrogen bonds: B:S.217, B:G.247, B:A.605

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M.F. et al., Potent competitive inhibition of human ribonucleotide reductase by a nonnucleoside small molecule. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-02

Peptides

Ribonucleoside-diphosphate reductase large subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonucleoside-diphosphate reductase large subunit

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