Structure of PDB 4kxl Chain B Binding Site BS02

Receptor Information

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

RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEGDQFIHEQNLNWLQQ
ADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAAD
GSRFQVWDYAEGEVETMLDRYFEAYL

Ligand information

• Ligand ID: 6C6
• InChI: InChI=1S/C15H22N5O7P/c21-11-9(5-26-28(23,24)25)27-15(12(11)22)20-7-18-10-13(16-6-17-14(10)20)19-8-3-1-2-4-8/h6-9,11-12,15,21-22H,1-5H2,(H,16,17,19)(H2,23,24,25)/t9-,11-,12-,15-/m1/s1
• InChIKey: ZLXWBMMFOMQXRH-SDBHATRESA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)NC4CCCC4
  ACDLabs 12.01: O=P(O)(O)OCC4OC(n2cnc1c(ncnc12)NC3CCCC3)C(O)C4O
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(NC4CCCC4)ncnc23
  CACTVS 3.370: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(NC4CCCC4)ncnc23
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)NC4CCCC4
• Formula: C15 H22 N5 O7 P
• Name: N-cyclopentyladenosine 5'-(dihydrogen phosphate)
• ChEMBL: CHEMBL1812058
• PDB chain: 4kxl Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4kxl N (6)-substituted AMPs inhibit mammalian deoxynucleotide N-hydrolase DNPH1.
• Resolution: 1.69 Å
• Binding residue (original residue number in PDB): C15 G16 S17 I18 R19 G20 I65 N69 S87 G89 E93
• Binding residue (residue number reindexed from 1): C6 G7 S8 I9 R10 G11 I40 N44 S62 G64 E68
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.6uM
  PDBbind-CN: -logKd/Ki=6.22,Kd=0.6uM

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