SMTL ID : 6l3r.2 (1 other biounit)

Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 4-bromo-N-((1S,2R)-2-(naphthalen-1-yl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)benzenesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

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

1 x E4X: 4-bromo-N-((1S,2R)-2-(naphthalen-1-yl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)benzenesulfonamide(Non-covalent)

E4X.2: 12 residues within 4Å: Chain A: W.611, E.612, I.613, S.614, Q.615, K.616, L.619, I.639, K.646, S.649, M.650, Y.653 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Q.615, A:K.616, A:K.616, A:K.616, A:L.619, A:K.646, A:M.650, A:Y.653 Hydrogen bonds: A:S.614, A:Q.615, A:K.616, A:K.646

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

TTP.3: 13 residues within 4Å: Chain A: D.153, S.154, I.155, I.158, I.182, R.183, I.189, A.190, G.191, T.192, S.196, N.197 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.155, A:I.158, A:I.189, A:T.192 Hydrogen bonds: A:D.153, A:I.155, A:A.190, A:G.191, A:N.197 Water bridges: A:R.183, A:R.183, A:S.196 Salt bridges: A:R.183

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: T.126, A.128, S.375, M.529, T.531, T.534 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.128 Hydrogen bonds: A:S.375, A:T.534

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: S.129, A.532, S.533 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.82, A:S.129, A:A.532, A:S.533, A:S.533, A:S.533

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyahara, S. et al., TAS1553, a novel small molecule ribonucleotide reductase (RNR) subunit interaction inhibitor, displays remarkable anti-tumor activity. To be published

Release Date

2020-10-28

Peptides

Ribonucleoside-diphosphate reductase large subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

Ribonucleoside-diphosphate reductase large subunit

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