Structure of PDB 5v1m Chain A Binding Site BS01

Receptor Information

>5v1m Chain A (length=185) Species: 9606 (Homo sapiens)

MGNWATHVYVPYEAKEEFLDLLDVLLPHAQTYVPRLVRMKVFHLSLSQSV
VLRHHWILPFVQALKARMTSFHRFFFTANQVKIYTNQEKTRTFIGLEVTS
GHAQFLDLVSEVDRVMEEFNLTTFYQDPSFHLSLAWCVGDARLQLEGQCL
QELQAIVDGFEVLLRVHTEQVRCKSGNKFFSMPLK

Ligand information

• Ligand ID: U5P
• InChI: InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: DJJCXFVJDGTHFX-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: URIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL214393
• DrugBank: DB03685
• ZINC: ZINC000002123545
• PDB chain: 5v1m Chain A Residue 308

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v1m Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities.
• Resolution: 1.47 Å
• Binding residue (original residue number in PDB): H120 S122 Y202 P205 S206 H208
• Binding residue (residue number reindexed from 1): H43 S45 Y125 P128 S129 H131
• Annotation score: 3

Enzymatic activity

• Enzyme Commision number: 4.6.1.-

Gene Ontology

Molecular Function

• GO:0004518 nuclease activity

Biological Process

• GO:0034477 U6 snRNA 3'-end processing

External links

• PDB: RCSB:5v1m, PDBe:5v1m, PDBj:5v1m
• PDBsum: 5v1m
• PubMed: 28887445
• UniProt: Q9BQ65|USB1_HUMAN U6 snRNA phosphodiesterase 1 (Gene Name=USB1)