Structure of PDB 4kxm Chain D Binding Site BS01

Receptor Information

>4kxm Chain D (length=132) Species: 10116 (Rattus norvegicus)

RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADGGDQFIHEQNL
NWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMI
RGAADGSRFQVWDYAEGEVETMLDRYFEAYLV

Ligand information

• Ligand ID: 6IA
• InChI: InChI=1S/C15H24N5O7P/c1-8(2)3-4-16-13-10-14(18-6-17-13)20(7-19-10)15-12(22)11(21)9(27-15)5-26-28(23,24)25/h6-9,11-12,15,21-22H,3-5H2,1-2H3,(H,16,17,18)(H2,23,24,25)/t9-,11-,12-,15-/m1/s1
• InChIKey: GZJXCRHEMLAMRA-SDBHATRESA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)NCCC(C)C)C(O)C3O
  CACTVS 3.341: CC(C)CCNc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  OpenEye OEToolkits 1.5.0: CC(C)CCNc1c2c(ncn1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O
  CACTVS 3.341: CC(C)CCNc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: CC(C)CCNc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
• Formula: C15 H24 N5 O7 P
• Name: N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE
• DrugBank: DB07205
• ZINC: ZINC000034390682
• PDB chain: 4kxm Chain C Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4kxm N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.
• Resolution: 2.24 Å
• Binding residue (original residue number in PDB): S117 M119
• Binding residue (residue number reindexed from 1): S97 M99
• Annotation score: 1
• Binding affinity: MOAD: Kd=2.6uM

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:4kxm, PDBe:4kxm, PDBj:4kxm
• PDBsum: 4kxm
• PubMed: 24260472
• UniProt: O35820|DNPH1_RAT 5-hydroxymethyl-dUMP N-hydrolase (Gene Name=Dnph1)