Structure of PDB 3dba Chain B Binding Site BS01

Receptor Information

>3dba Chain B (length=171) Species: 9031 (Gallus gallus)

RLEECNILFELLTEIQDEAGSMEKIVHKTLQRLSQLLAADRCSMFICRSR
NGIPEVATRLLNVTPTSKFEDNLVNPDKETVFPLDIGIAGWVAHTKKFFN
IPDVKKNNHFSDYLDKKTGYTTVNMMAIPITQGKEVLAVVMALNKLNASE
FSKEDEEVFKKYLNFISLVLR

Ligand information

• Ligand ID: 35G
• 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 1.7.0: c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
  CACTVS 3.370: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]4[C@H]3O
  ACDLabs 12.01: O=C4NC(=Nc1c4ncn1C3OC2COP(=O)(OC2C3O)O)N
  OpenEye OEToolkits 1.7.0: c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O4)O)O)N=C(NC2=O)N
  CACTVS 3.370: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
• Formula: C10 H12 N5 O7 P
• Name: GUANOSINE-3',5'-MONOPHOSPHATE
• ChEMBL: CHEMBL395336
• DrugBank: DB02315
• ZINC: ZINC000004095501
• PDB chain: 3dba Chain B Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dba The Structure of the GAF A Domain from Phosphodiesterase 6C Reveals Determinants of cGMP Binding, a Conserved Binding Surface, and a Large cGMP-dependent Conformational Change.
• Resolution: 2.57 Å
• Binding residue (original residue number in PDB): S97 F99 L115 N116 I142 A143 F164 S165 L168 T176 M179 L197
• Binding residue (residue number reindexed from 1): S43 F45 L61 N62 I88 A89 F110 S111 L114 T122 M125 L143
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=8.00,Kd=10nM

Enzymatic activity

• Enzyme Commision number: 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.

External links

• PDB: RCSB:3dba, PDBe:3dba, PDBj:3dba
• PDBsum: 3dba
• PubMed: 18614542
• UniProt: P52731|PDE6C_CHICK Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' (Gene Name=PDE6C)