Structure of PDB 8ugs Chain B Binding Site BS03

Receptor Information
>8ugs Chain B (length=816) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVHRFLDQNPGFADQYFGRKLSPEDVANACEDGCPEGCTSFRELCQVEES
AALFELVQDMQENVNMERVVFKILRRLCSILHADRCSLFMYRQRNGVAEL
ATRLFSVQPDSVLEDCLVPPDSEIVFPLDIGVVGHVAQTKKMVNVQDVME
CPHFSSFADELTDYVTRNILATPIMNGKDVVAVIMAVNKLDGPCFTSEDE
DVFLKYLNFGTLNLKIYHLSYLHNCETRRGQVLLWSANKVFEELTDIERQ
FHKAFYTVRAYLNCDRYSVGLLDMTKEKEFFDVWPVLMGEAQAYSGPRTP
DGREILFYKVIDYILHGKEDIKVIPSPPADHWALASGLPTYVAESGFICN
IMNAPADEMFNFQEGPLDDSGWIVKNVLSMPIVNKKEEIVGVATFYNRKD
GKPFDEQDEVLMESLTQFLGWSVLNTDTYDKMNKLENRKDIAQDMVLYHV
RCDREEIQLILPTRERLGKEPADCEEDELGKILKEVLPGPAKFDIYEFHF
SDLECTELELVKCGIQMYYELGVVRKFQIPQEVLVRFLFSVSKGYRRITY
HNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDIDHRGTNN
LYQMKSQNPLAKLHGSSILERHHLEFGKFLLSEETLNIYQNLNRRQHEHV
IHLMDIAIIATDLALYFKKRTMFQKIVDESKNYEDRKSWVEYLSLETTRK
EIVMAMMMTACDLSAITKPWEVQSKVALLVAAEFWEQGDLERTVLDQQPI
PMMDRNKAAELPKLQVGFIDFVCTFVYKEFSRFHEEILPMFDRLQNNRKE
WKALADEYEAKVKALE
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 chain8ugs Chain B Residue 904 [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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PDB8ugs Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		H557 H561 D598 L669 D718 L719 F774
Binding residue
(residue number reindexed from 1)		H551 H555 D592 L663 D712 L713 F768
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:0043153 entrainment of circadian clock by photoperiod
GO:0060041 retina development in camera-type eye
Cellular Component
GO:0001750 photoreceptor outer segment
GO:0016020 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:8ugs, PDBe:8ugs, PDBj:8ugs
PDBsum8ugs
PubMed38159849
UniProtP23439|PDE6B_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (Gene Name=PDE6B)

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