Ligand · Y3G

Y3G · 5-ethynylpyrimidine-2,4(1H,3H)-dione

Y3G, 5-ethynylpyrimidine-2,4(1H,3H)-dione (C6 H4 N2 O2, 136.1 g/mol), in the MolNFT structures on GenesisL1: bound in 6 records (3 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands…

Component: Y3G
Formula: C6 H4 N2 O2
Class: ligand
Structures: 6
PDB entries: 3

Binding sites

Y3G in 6 structures; the first of them:

7LJS · Porcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Ethynyluracil (5EU) - Open… · Y3G A1107 · binds ASN609, GLU611, LEU612, ILE613, ASN668, SER670, ASN736, THR737
7LJT · Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH… · Y3G A1107 · binds LYS574, ASN609, GLU611, LEU612, ILE613, ASN668, SER670, ASN736 and 1 more
7LJU · Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU) · Y3G A1106 · binds ASN609, GLU611, LEU612, ILE613, ASN668, SER670, ASN736, THR737
7LJS · Porcine dihydropyrimidine dehydrogenase (dpd) complexed with 5- ethynyluracil (5EU)… · Y3G A1107 · binds ASN609, GLU611, LEU612, ILE613, ASN668, SER670, ASN736, THR737
7LJT · Porcine dihydropyrimidine dehydrogenase (dpd) soaked with 5- ethynyluracil (5EU), NADPH… · Y3G A1107 · binds ASN609, GLU611, LEU612, ILE613, ASN668, SER670, ASN736, THR737
7LJU · Porcine dihydropyrimidine dehydrogenase (dpd) crosslinked with 5- ethynyluracil (5EU) · Y3G A1106 · binds ASN609, GLU611, LEU612, ILE613, ASN668, SER670, ASN736, THR737

Residues it binds most

ASN 24, THR 24, GLU 24, ILE 24, LEU 24, SER 23, CYS 6, MET 4, GLY 3, LYS 3 (residue and the binding sites it lines).

Found with

FAD · Flavin-adenine dinucleotide
SF4 · Iron/sulfur cluster
FMN · Flavin mononucleotide
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate
FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol

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