Structure of PDB 5c8w Chain D Binding Site BS01

Receptor Information

>5c8w Chain D (length=119) Species: 9606 (Homo sapiens)

VRKDSSEKKLITDALNKNQFLKRLDPQQIKDMVECMYGRNYQQGSYIIKQ
GEPGNHIFVLAEGRLEVFQGEKLLSSIPMWTTFGELAILYNCTRTASVKA
ITNVKTWALDREVFQNIMR

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: 5c8w Chain D Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5c8w Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): F231 G232 L234 A235 R242 T243
• Binding residue (residue number reindexed from 1): F83 G84 L86 A87 R94 T95
• Annotation score: 1
• Binding affinity: MOAD: Kd=43.8nM

Enzymatic activity

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

External links

• PDB: RCSB:5c8w, PDBe:5c8w, PDBj:5c8w
• PDBsum: 5c8w
• PubMed: 26769964
• UniProt: Q13237|KGP2_HUMAN cGMP-dependent protein kinase 2 (Gene Name=PRKG2)