Structure of PDB 3od0 Chain A Binding Site BS01

Receptor Information

>3od0 Chain A (length=127) Species: 9606 (Homo sapiens)

SHVTLPFYPKSPQSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGK
DSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCT
RTATVKTLVNVKLWAIDRQCFQTIMMR

Ligand information

• Ligand ID: PCG
• InChI: InChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
• InChIKey: ZOOGRGPOEVQQDX-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
  ACDLabs 10.04: O=C4NC(=Nc1c4ncn1C3OC2COP(=O)(OC2C3O)O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)O)O)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]4[C@H]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
• Formula: C10 H12 N5 O7 P
• Name: CYCLIC GUANOSINE MONOPHOSPHATE
• ChEMBL: CHEMBL395336
• DrugBank: DB02315
• ZINC: ZINC000004095501
• PDB chain: 3od0 Chain A Residue 250

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3od0 Co-Crystal Structures of PKG Ibeta (92-227) with cGMP and cAMP Reveal the Molecular Details of Cyclic-Nucleotide Binding
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): L172 F181 G182 E183 L184 A185 R192 T193
• Binding residue (residue number reindexed from 1): L81 F90 G91 E92 L93 A94 R101 T102
• Annotation score: 1
• Binding affinity: Manual survey: Kd=12+-1.6nM (21526164)
  PDBbind-CN: -logKd/Ki=7.92,Kd=12nM

Enzymatic activity

• Enzyme Commision number: 2.7.11.12: cGMP-dependent protein kinase.

External links

• PDB: RCSB:3od0, PDBe:3od0, PDBj:3od0
• PDBsum: 3od0
• PubMed: 21526164
• UniProt: Q13976|KGP1_HUMAN cGMP-dependent protein kinase 1 (Gene Name=PRKG1)