Structure of PDB 8pqr Chain D Binding Site BS02

Receptor Information

>8pqr Chain D (length=152) Species: 251229 (Chroococcidiopsis thermalis PCC 7203)

KRKIIYLASPYGFSQQQKTLLLPPIVRALEALGIEVWEPFARNNQIDFSQ
ADWAYRVAQADLQDVKNCDGIFAVVNGTPPDEGVMVELGMAIALNKAIFL
FRDDFRRCSDNERYPLNLMLFAGLPEIGWENYYYTSVDEIQSHDKALYKW
LT

Ligand information

• Ligand ID: DIH
• InChI: InChI=1S/C12H16N4O3/c17-5-8-3-16(4-9(8)18)2-7-1-13-11-10(7)14-6-15-12(11)19/h1,6,8-9,13,17-18H,2-5H2,(H,14,15,19)/p+1/t8-,9+/m1/s1
• InChIKey: AFNHHLILYQEHKK-BDAKNGLRSA-O
• SMILES:
  OpenEye OEToolkits 2.0.6: c1c(c2c([nH]1)C(=O)NC=N2)C[NH+]3CC(C(C3)O)CO
  OpenEye OEToolkits 2.0.6: c1c(c2c([nH]1)C(=O)NC=N2)C[NH+]3C[C@@H]([C@H](C3)O)CO
  CACTVS 3.385: OC[CH]1C[NH+](C[CH]1O)Cc2c[nH]c3C(=O)NC=Nc23
  CACTVS 3.385: OC[C@H]1C[NH+](C[C@@H]1O)Cc2c[nH]c3C(=O)NC=Nc23
• Formula: C12 H17 N4 O3
• Name: 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one
• PDB chain: 8pqr Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pqr Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase
• Resolution: 1.586 Å
• Binding residue (original residue number in PDB): S10 F14 P40 F41 N44 V58 D62 D82 G84 V85 E88
• Binding residue (residue number reindexed from 1): S9 F13 P39 F40 N43 V57 D61 D81 G83 V84 E87
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0046872 metal ion binding
• GO:0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity

Biological Process

• GO:0009159 deoxyribonucleoside monophosphate catabolic process

External links

• PDB: RCSB:8pqr, PDBe:8pqr, PDBj:8pqr
• PDBsum: 8pqr
• PubMed: 38449528
• UniProt: K9TVX3