Structure of PDB 4kxn Chain B Binding Site BS01

Receptor Information

>4kxn Chain B (length=126) Species: 10116 (Rattus norvegicus)

RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTGDQFIHEQNLNWLQQA
DVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADG
SRFQVWDYAEGEVETMLDRYFEAYLV

Ligand information

• Ligand ID: 6K6
• InChI: InChI=1S/C15H18N5O8P/c21-11-9(5-27-29(23,24)25)28-15(12(11)22)20-7-19-10-13(17-6-18-14(10)20)16-4-8-2-1-3-26-8/h1-3,6-7,9,11-12,15,21-22H,4-5H2,(H,16,17,18)(H2,23,24,25)/t9-,11-,12-,15-/m1/s1
• InChIKey: WDFCXEWULSQTFC-SDBHATRESA-N
• SMILES:
  CACTVS 3.370: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(NCc4occc4)ncnc23
  OpenEye OEToolkits 1.7.6: c1cc(oc1)CNc2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(O)O)O)O
  OpenEye OEToolkits 1.7.6: c1cc(oc1)CNc2c3c(ncn2)n(cn3)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OCC4OC(n2cnc1c(ncnc12)NCc3occc3)C(O)C4O
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(NCc4occc4)ncnc23
• Formula: C15 H18 N5 O8 P
• Name: N-(furan-2-ylmethyl)adenosine 5'-(dihydrogen phosphate)
• PDB chain: 4kxn Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4kxn N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): C15 G16 I18 R19 I65 N69 S87 G89 E93
• Binding residue (residue number reindexed from 1): C6 G7 I9 R10 I39 N43 S61 G63 E67
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.8uM
  PDBbind-CN: -logKd/Ki=6.10,Kd=0.8uM

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