Structure of PDB 4fyk Chain D Binding Site BS02

Receptor Information

>4fyk Chain D (length=124) Species: 10116 (Rattus norvegicus)

RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGDQFIHEQNLNWLQQA
DVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADG
SRFQVWDYAEGEVETMLDRYFEAL

Ligand information

• Ligand ID: SRA
• InChI: InChI=1S/C10H14N5O6PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(21-10)1-20-22(18,19)23/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,23)/t4-,6-,7-,10-/m1/s1
• InChIKey: UBCPYVAQZGCDJO-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=S)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=S)[CH](O)[CH]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=S)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=S)[C@@H](O)[C@H]3O
  ACDLabs 10.04: S=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C10 H14 N5 O6 P S
• Name: ADENOSINE -5'-THIO-MONOPHOSPHATE
• ChEMBL: CHEMBL574816
• PDB chain: 4fyk Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4fyk Structure of the oncoprotein Rcl bound to three nucleotide analogues.
• Resolution: 1.79 Å
• Binding residue (original residue number in PDB): G16 I18 R19 I65 N69 S87 G89 E93
• Binding residue (residue number reindexed from 1): G7 I9 R10 I39 N43 S61 G63 E67
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.2.-

Gene Ontology

Molecular Function

• GO:0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity

Biological Process

• GO:0009159 deoxyribonucleoside monophosphate catabolic process

External links

• PDB: RCSB:4fyk, PDBe:4fyk, PDBj:4fyk
• PDBsum: 4fyk
• PubMed: 23385460
• UniProt: O35820|DNPH1_RAT 5-hydroxymethyl-dUMP N-hydrolase (Gene Name=Dnph1)