Structure of PDB 8ugb Chain A Binding Site BS02

Receptor Information
>8ugb Chain A (length=811) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEVEKFLDSNVSFAKQYYNLRYRAKVISDLLGPREAAVDFSNYHALNSVE
ESEIIFDLLRDFQDNLQAEKCVFNVMKKLCFLLQADRMSLFMYRARNGIA
ELATRLFNVHKDAVLEECLVAPDSEIVFPLDMGVVGHVALSKKIVNVPNT
EEDEHFCDFVDTLTEYQTKNILASPIMNGKDVVAIIMVVNKVDGPHFTEN
DEEILLKYLNFANLIMKVFHLSYLHNCETRRGQILLWSGSKVFEELTDIE
RQFHKALYTVRAFLNCDRYSVGLLDMTKQKEFFDVWPVLMGEAPPYAGPR
TPDGREINFYKVIDYILHGKEDIKVIPNPPPDHWALVSGLPTYVAQNGLI
CNIMNAPSEDFFAFQKEPLDESGWMIKNVLSMPIVNKKEEIVGVATFYNR
KDGKPFDEMDETLMESLTQFLGWSVLNPDTYELMNKLENRKDIFQDMVKY
HVKCDNEEIQTILKTREVYGKEPWECEEEELAEILQGELPDADKYEINKF
HFSDLPLTELELVKCGIQMYYELKVVDKFHIPQEALVRFMYSLSKGYRRI
TYHNWRHGFNVGQTMFSLLVTGKLKRYFTDLEALAMVTAAFCHDIDHRGT
NNLYQMKSQNPLAKLHGSSILERHHLEFGKTLLRDESLNIFQNLNRRQHE
HAIHMMDIAIIATDLALYFKKRTMFQKIVDQSKTYETQQEWTQYMMLDQT
RKEIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLQQN
PIPMMDRNKADELPKLQVGFIDFVCTFVYKEFSRFHEEITPMLDGITNNR
KEWKALADEYE
Ligand information
Ligand IDPCG
InChIInChI=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
InChIKeyZOOGRGPOEVQQDX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C4NC(=Nc1c4ncn1C3OC2COP(=O)(OC2C3O)O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]4[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
FormulaC10 H12 N5 O7 P
NameCYCLIC GUANOSINE MONOPHOSPHATE
ChEMBLCHEMBL395336
DrugBankDB02315
ZINCZINC000004095501
PDB chain8ugb Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ugb Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		S95 F97 F113 N114 F134 V140 V141 C163 V166 T170 Y172 M193 V195
Binding residue
(residue number reindexed from 1)		S89 F91 F107 N108 F128 V134 V135 C157 V160 T164 Y166 M187 V189
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity
GO:0004117 calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity
GO:0048101 calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity
Biological Process
GO:0007165 signal transduction
GO:0007601 visual perception
GO:0019933 cAMP-mediated signaling
GO:0060041 retina development in camera-type eye
Cellular Component
GO:0001750 photoreceptor outer segment
GO:0005886 plasma membrane
GO:0042622 photoreceptor outer segment membrane
GO:0042995 cell projection
GO:0097381 photoreceptor disc membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ugb, PDBe:8ugb, PDBj:8ugb
PDBsum8ugb
PubMed38159849
UniProtP11541|PDE6A_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (Gene Name=PDE6A)

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