Structure of PDB 8ugb Chain B Binding Site BS04

Receptor Information
>8ugb Chain B (length=811) 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
WKALADEYEAK
Ligand information
Ligand IDZUD
InChIInChI=1S/C25H36N6O4S/c1-5-8-20-22-23(31(4)29-20)25(32)28-24(27-22)19-16-18(10-11-21(19)35-15-6-2)36(33,34)26-13-12-17-9-7-14-30(17)3/h10-11,16-17,26H,5-9,12-15H2,1-4H3,(H,27,28,32)/t17-/m1/s1
InChIKeyIYFNEFQTYQPVOC-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCOc1ccc(cc1C2=NC(=O)c3n(C)nc(CCC)c3N2)[S](=O)(=O)NCC[CH]4CCCN4C
ACDLabs 12.01CN1CCCC1CCNS(=O)(=O)c1cc(C2=NC(=O)c3c(N2)c(nn3C)CCC)c(OCCC)cc1
OpenEye OEToolkits 2.0.7CCCc1c2c(n(n1)C)C(=O)N=C(N2)c3cc(ccc3OCCC)S(=O)(=O)NCCC4CCCN4C
OpenEye OEToolkits 2.0.7CCCc1c2c(n(n1)C)C(=O)N=C(N2)c3cc(ccc3OCCC)S(=O)(=O)NCC[C@H]4CCCN4C
CACTVS 3.385CCCOc1ccc(cc1C2=NC(=O)c3n(C)nc(CCC)c3N2)[S](=O)(=O)NCC[C@H]4CCCN4C
FormulaC25 H36 N6 O4 S
NameUdenafil;
(3P)-3-(1-methyl-7-oxo-3-propyl-4,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)-N-{2-[(2R)-1-methylpyrrolidin-2-yl]ethyl}-4-propoxybenzene-1-sulfonamide
ChEMBL
DrugBank
ZINC
PDB chain8ugb 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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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)		F740 M758 L767 L770 Q771 F774
Binding residue
(residue number reindexed from 1)		F734 M752 L761 L764 Q765 F768
Annotation score1
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:8ugb, PDBe:8ugb, PDBj:8ugb
PDBsum8ugb
PubMed38159849
UniProtP23439|PDE6B_BOVIN Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (Gene Name=PDE6B)

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