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Ligand · DUD

DUD · Deoxyuridine-5'-diphosphate

DUD, Deoxyuridine-5'-diphosphate (C9 H14 N2 O11 P2, 388.2 g/mol), in the MolNFT structures on GenesisL1: bound in 32 records (16 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands…

Component
DUD
Formula
C9 H14 N2 O11 P2
Class
ligand
Structures
32
PDB entries
16

Binding sites

DUD in 32 structures; the first of them:

  • 1DUC · Eiav dutpase DUDP/STRONTIUM complex · DUD A201 · binds ASN67, GLY68, GLY69, ILE70, ILE71, ASP72, TYR75, GLU78 and 3 more
  • 1DUD · Deoxyuridine 5'-triphosphate nucleotide hydrolase (D-utpase) complexed with the substrate… · DUD A153 · binds MET68, ASN84, GLY87, LEU88, ILE89, ASP90, TYR93, GLN96 and 2 more
  • 1OGK · The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP · DUD B1280 · binds LYS60, TRP61, TRP62, LYS63, GLN22, LEU25, ASN26, MET29 and 13 more
  • 1Q5H · Human dUTP Pyrophosphatase complex with dUDP · DUD A779 · binds VAL59, GLY74, ALA75, GLY76, VAL77, ILE78, ASP79, TYR82 and 13 more
  • 1SLH · Mycobacterium tuberculosis dUTPase complexed with magnesium and dUDP · DUD A2170 · binds VAL61, ASN77, GLY80, THR81, ILE82, ASP83, TYR86, GLU89 and 8 more
  • 2HR6 · Crystal structure of dUTPase in complex with substrate analogue dUDP and manganese · DUD A777 · binds MET68, ASN84, GLY87, LEU88, ILE89, ASP90, TYR93, GLN96 and 2 more
  • 2OL0 · High Resolution Crystal Structures of Vaccinia Virus dUTPase · DUD B1202 · binds ARG69, SER70, GLY71, ARG111, ILE66, GLY80, GLY81, GLY82 and 8 more
  • 2Y1T · Bacillus subtilis prophage dUTPase in complex with dUDP · DUD B143 · binds SER62, SER63, GLN72, ASN74, GLY77, VAL78, ILE79, TYR83 and 4 more
  • 2YZJ · Crystal structure of dCTP deaminase from Sulfolobus tokodaii · DUD A6194 · binds ILE97, THR113, VAL114, ILE115, ASP116, TYR119, VAL123, ASN124 and 10 more
  • 3C2T · Evolution of chlorella virus dUTPase · DUD A777 · binds LEU75, ALA76, GLY77, VAL78, ILE79, ASP80, TYR83, GLU86 and 3 more
  • 3C3I · Evolution of chlorella virus dUTPase · DUD A776 · binds LEU75, ALA76, GLY77, VAL78, ILE79, ASP80, TYR83, GLU86 and 4 more
  • 3CA9 · Evolution of chlorella virus dUTPase · DUD A777 · binds ILE60, LEU75, ALA76, GLY77, VAL78, ILE79, ASP80, TYR83 and 4 more
  • 3ELH · X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase… · DUD A160 · binds LYS9, TYR50, HIS53, TYR58, ASN62, ARG86, GLN89, ARG99 and 3 more
  • 3FCV · Crystal structure of the Mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with dUDP · DUD A201 · binds LYS9, TYR50, HIS53, TYR58, LEU62, ARG86, GLN89, THR92 and 4 more
  • 4AMB · Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater · DUD B1391 · binds SER24, LEU27, ASN212, THR233, GLY235, SER236, ILE237, THR264 and 11 more

Residues it binds most

GLY 66, ILE 80, TYR 80, ARG 60, ASN 68, VAL 50, LYS 54, SER 46, ASP 52, GLN 54 (residue and the binding sites it lines).

Found with

  • MG · Magnesium ion
  • EDO · 1,2-ethanediol
  • TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol
  • MN · Manganese (II) ion
  • SR · Strontium ion
  • CL · Chloride ion

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