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Ligand · UM3

UM3 · 2'-deoxyuridine 3'-monophosphate

UM3, 2'-deoxyuridine 3'-monophosphate (C9 H13 N2 O8 P, 308.2 g/mol), in the MolNFT structures on GenesisL1: bound in 8 records (4 PDB entries). Every binding site with its residues within 4.5 Å, the residues it binds most and the ligands…

Component
UM3
Formula
C9 H13 N2 O8 P
Class
ligand
Structures
8
PDB entries
4

Binding sites

UM3 in 8 structures; the first of them:

  • 1W4P · Binding of Nonnatural 3'-Nucleotides to Ribonuclease A · UM3 A1125 · binds LYS7, GLN11, HIS12, LYS41, VAL43, ASN44, THR45, ASP83 and 4 more
  • 2DJH · Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 · UM3 A118 · binds LYS25, SER52, PHE53, ASP54, LYS55, ARG56, SER57, LYS60 and 6 more
  • 2RNF · X-ray crystal structure of human ribonuclease 4 in complex with D(UP) · UM3 A301 · binds ARG7, GLN11, HIS12, LYS40, PHE42, ASN43, THR44, ASP80 and 5 more
  • 3VJ7 · Crystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant · UM3 A117 · binds LYS25, SER52, PHE53, ASP54, LYS55, ARG56, SER57, LYS60 and 6 more
  • 1W4P · Binding of nonnatural 3'-nucleotides to ribonuclease a · UM3 A1125 · binds LYS7, GLN11, HIS12, LYS41, VAL43, ASN44, THR45, ASP83 and 4 more
  • 2DJH · Crystal structure of the carboxy-terminal ribonuclease domain of colicin E5 · UM3 A118 · binds LYS25, SER52, PHE53, ASP54, LYS55, ARG56, SER57, LYS60 and 6 more
  • 2RNF · X-ray crystal structure of human ribonuclease 4 in complex with D(UP) · UM3 A301 · binds ARG7, GLN11, HIS12, LYS40, PHE42, ASN43, THR44, ASP80 and 5 more
  • 3VJ7 · Crystal structure of the carboxy-terminal ribonuclease domain of colicin E5 R33Q mutant · UM3 A117 · binds LYS25, SER52, PHE53, ASP54, LYS55, ARG56, SER57, LYS60 and 6 more

Residues it binds most

LYS 12, ASP 12, ARG 8, HIS 8, PHE 12, GLN 12, THR 12, ASN 8, SER 4, VAL 8 (residue and the binding sites it lines).

Found with

  • 3PD · 2-amino-9-(2-deoxy-3-O-phosphonopentofuranosyl)-1,9-dihydro-6H-purin-6-one

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