SMTL ID : 6l7l.1 (1 other biounit)

Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 5-chloro-2-(N-((1S,2R)-2-(2,3-dihydro-1H-inden-4-yl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)sulfamoyl)benzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.153 Ligands: TTP.2 No protein-ligand interaction detected (PLIP)

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

TTP.2: 13 residues within 4Å: Chain A: D.153, S.154, I.155, E.156, I.158, I.182, R.183, I.189, A.190, S.196, N.197, G.198 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.155, A:I.158, A:I.189 Hydrogen bonds: A:D.153, A:I.155, A:R.183, A:A.190, A:N.197, A:G.198 Water bridges: A:S.196, A:S.196 Salt bridges: A:R.183

1 x E6O: 5-chloro-2-(N-((1S,2R)-2-(2,3-dihydro-1H-inden-4-yl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)sulfamoyl)benzamide(Non-covalent)

E6O.3: 15 residues within 4Å: Chain A: V.610, W.611, E.612, I.613, S.614, Q.615, K.616, L.619, H.638, I.639, A.640, K.646, S.649, M.650, Y.653 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.615, A:K.616, A:K.616, A:L.619, A:K.646, A:M.650, A:Y.653 Hydrogen bonds: A:I.613, A:S.614, A:Q.615, A:Q.615, A:K.616, A:A.640, A:K.646

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

ACT.4: 7 residues within 4Å: Chain A: T.126, A.128, S.375, M.529, T.531, T.534 Ligands: ACT.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.128 Hydrogen bonds: A:T.534 ACT.5: 3 residues within 4Å: Chain A: Q.457, T.503, D.504 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.504 ACT.6: 3 residues within 4Å: Chain A: S.129, S.533 Ligands: ACT.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.129, A:S.533, A:S.533 Water bridges: A:T.531, A:T.534 ACT.7: 4 residues within 4Å: Chain A: R.340, K.341, G.658 Ligands: ACT.8 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.340, A:K.341 ACT.8: 2 residues within 4Å: Chain A: W.655 Ligands: ACT.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.655

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

2020-11-04

Peptides

Ribonucleoside-diphosphate reductase large subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonucleoside-diphosphate reductase large subunit

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