Structure of PDB 5khk Chain A Binding Site BS01

Receptor Information

>5khk Chain A (length=201) Species: 10090 (Mus musculus)

DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSIL
GELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGD
YIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRT
ASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSI
L

Ligand information

• Ligand ID: 6SZ
• InChI: InChI=1S/C10H12N5O6P/c11-10-12-1-4-8(14-10)15(3-13-4)9-6(16)7-5(20-9)2-19-22(17,18)21-7/h1,3,5-7,9,16H,2H2,(H,17,18)(H2,11,12,14)/t5-,6-,7-,9-/m1/s1
• InChIKey: ZZUVWWINFTZMGV-JXOAFFINSA-N
• SMILES:
  CACTVS 3.385: Nc1ncc2ncn([C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]4[C@H]3O)c2n1
  OpenEye OEToolkits 2.0.5: c1c2c(nc(n1)N)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)COP(=O)(O4)O)O
  OpenEye OEToolkits 2.0.5: c1c2c(nc(n1)N)n(cn2)C3C(C4C(O3)COP(=O)(O4)O)O
  CACTVS 3.385: Nc1ncc2ncn([CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O)c2n1
• Formula: C10 H12 N5 O6 P
• Name: 2-Aminopurine riboside-3',5'-cyclic monophosphate;
  2-NH2-cPuMP
• ZINC: ZINC000038580933
• PDB chain: 5khk Chain A Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5khk Cyclic Purine and Pyrimidine Nucleotides Bind to the HCN2 Ion Channel and Variably Promote C-Terminal Domain Interactions and Opening.
• Resolution: 2.07 Å
• Binding residue (original residue number in PDB): V564 M572 F580 G581 E582 I583 C584 R591 T592 A593 R632 I636
• Binding residue (residue number reindexed from 1): V122 M130 F138 G139 E140 I141 C142 R149 T150 A151 R190 I194
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.41uM
  PDBbind-CN: -logKd/Ki=6.39,Kd=0.41uM

External links

• PDB: RCSB:5khk, PDBe:5khk, PDBj:5khk
• PDBsum: 5khk
• PubMed: 27568927
• UniProt: O88703|HCN2_MOUSE Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (Gene Name=Hcn2)