Structure of PDB 1s3f Chain B Binding Site BS01

Receptor Information

>1s3f Chain B (length=167) Species: 1587 (Lactobacillus helveticus)

MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFT
DPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAF
EIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLAD
YNFNECPSNPVRGYGIY

Ligand information

• Ligand ID: SNI
• InChI: InChI=1S/C10H12N4O4Se/c15-1-4-6(16)7(17)10(18-4)14-3-13-5-8(14)11-2-12-9(5)19/h2-4,6-7,10,15-17H,1H2,(H,11,12,19)/t4-,6-,7-,10-/m1/s1
• InChIKey: MXLAAGNIPFEHEI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)CO)O)O)N=CNC2=[Se]
  CACTVS 3.341: OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=[Se])NC=Nc23
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=CNC2=[Se]
  ACDLabs 10.04: [Se]=C1c2ncn(c2N=CN1)C3OC(C(O)C3O)CO
  CACTVS 3.341: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=[Se])NC=Nc23
• Formula: C10 H12 N4 O4 Se
• Name: 9-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-1,9-DIHYDRO-PURINE-6-THIONE;
  SELENOINOSINE
• DrugBank: DB02753
• PDB chain: 1s3f Chain B Residue 746

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1s3f Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): S14 P44 W67 T71 D75 D95 G97 S98 E101
• Binding residue (residue number reindexed from 1): S14 P44 W67 T71 D75 D95 G97 S98 E101
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y11 D75 D95 E101
• Catalytic site (residue number reindexed from 1): Y11 D75 D95 E101
• Enzyme Commision number: 2.4.2.6: nucleoside deoxyribosyltransferase.

Gene Ontology

Molecular Function

• GO:0016757 glycosyltransferase activity
• GO:0050144 nucleoside deoxyribosyltransferase activity

External links

• PDB: RCSB:1s3f, PDBe:1s3f, PDBj:1s3f
• PDBsum: 1s3f
• PubMed: 14992575
• UniProt: Q8RLY5