Structure of PDB 8qhq Chain F Binding Site BS01

Receptor Information

>8qhq Chain F (length=132) Species: 9606 (Homo sapiens)

RPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAEGGDRLIHE
QDLEWLQQADVVVAEVTQPSLGVGYQLGRAVAFNKRILCLFRPQSGRVLS
AMIRGAADGSRFQVWDYEEGEVEALLDRYFEA

Ligand information

• Ligand ID: 5HU
• InChI: InChI=1S/C10H15N2O9P/c13-3-5-2-12(10(16)11-9(5)15)8-1-6(14)7(21-8)4-20-22(17,18)19/h2,6-8,13-14H,1,3-4H2,(H,11,15,16)(H2,17,18,19)/t6-,7+,8+/m0/s1
• InChIKey: WEBVWKFGRVLCNS-XLPZGREQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=C(C(=O)NC2=O)CO)COP(=O)(O)O)O
  CACTVS 3.341: OCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)CO)COP(=O)(O)O)O
  CACTVS 3.341: OCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1CO)C2OC(C(O)C2)COP(=O)(O)O
• Formula: C10 H15 N2 O9 P
• Name: 5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL1160818
• DrugBank: DB03846
• ZINC: ZINC000013538464
• PDB chain: 8qhq Chain F Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qhq Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): C26 G27 S28 I29 R30 H56 V57 I76 S98 G100 Q104
• Binding residue (residue number reindexed from 1): C7 G8 S9 I10 R11 H37 V38 I48 S70 G72 Q76
• Annotation score: 2

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:8qhq, PDBe:8qhq, PDBj:8qhq
• PDBsum: 8qhq
• PubMed: 37884503
• UniProt: O43598|DNPH1_HUMAN 5-hydroxymethyl-dUMP N-hydrolase (Gene Name=DNPH1)