Structure of PDB 5e8f Chain A Binding Site BS02

Receptor Information
>5e8f Chain A (length=147) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKI
LKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTN
TWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Ligand information
Ligand IDGER
InChIInChI=1S/C20H34/c1-7-18(4)12-9-14-20(6)16-10-15-19(5)13-8-11-17(2)3/h7,11,14-15H,8-10,12-13,16H2,1-6H3/b18-7+,19-15+,20-14+
InChIKeyHSOYJGBJQAKCNA-CAIKYXSQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04C(=C/CCC(=C/C)/C)(\CC/C=C(/CC/C=C(\C)C)C)C
OpenEye OEToolkits 1.5.0C\C=C(/C)\CC\C=C(/C)\CC\C=C(/C)\CCC=C(C)C
CACTVS 3.341
OpenEye OEToolkits 1.5.0		CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
CACTVS 3.341C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C
FormulaC20 H34
NameGERAN-8-YL GERAN
ChEMBL
DrugBank
ZINCZINC000014880577
PDB chain5e8f Chain D Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5e8f The N- and C-terminal ends of RPGR can bind to PDE6 delta.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		M20 S39 Q78 I129 T131 F133
Binding residue
(residue number reindexed from 1)		M17 S36 Q75 I126 T128 F130
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0005095 GTPase inhibitor activity
GO:0005515 protein binding
GO:0031267 small GTPase binding
Biological Process
GO:0007601 visual perception
GO:0050953 sensory perception of light stimulus
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5e8f, PDBe:5e8f, PDBj:5e8f
PDBsum5e8f
PubMed26553937
UniProtO43924|PDE6D_HUMAN Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (Gene Name=PDE6D)

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