Structure of PDB 1gdd Chain A Binding Site BS01

Receptor Information
>1gdd Chain A (length=324) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHE
AGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLF
VLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLND
LDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVVTAIIFC
VALSDYDLVMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKK
SPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTK
NVQFVFDAVTDVIIKNNLKDCGLF
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain1gdd Chain A Residue 355 [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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PDB1gdd Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		E43 S44 G45 K46 S47 T48 L175 R176 T177 R178 N269 K270 D272 C325 A326 T327
Binding residue
(residue number reindexed from 1)		E35 S36 G37 K38 S39 T40 L167 R168 T169 R170 N239 K240 D242 C295 A296 T297
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E43 T48 R178 D200
Catalytic site (residue number reindexed from 1) E35 T40 R170 D192
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001664 G protein-coupled receptor binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019001 guanyl nucleotide binding
GO:0019003 GDP binding
GO:0031683 G-protein beta/gamma-subunit complex binding
GO:0031749 D2 dopamine receptor binding
GO:0031821 G protein-coupled serotonin receptor binding
GO:0032794 GTPase activating protein binding
GO:0046872 metal ion binding
Biological Process
GO:0007165 signal transduction
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007188 adenylate cyclase-modulating G protein-coupled receptor signaling pathway
GO:0043949 regulation of cAMP-mediated signaling
GO:0050805 negative regulation of synaptic transmission
GO:0051301 cell division
GO:0060236 regulation of mitotic spindle organization
GO:0099645 neurotransmitter receptor localization to postsynaptic specialization membrane
GO:1904322 cellular response to forskolin
GO:1904778 positive regulation of protein localization to cell cortex
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005834 heterotrimeric G-protein complex
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005938 cell cortex
GO:0030496 midbody
GO:0032991 protein-containing complex
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1gdd, PDBe:1gdd, PDBj:1gdd
PDBsum1gdd
PubMed7481799
UniProtP10824|GNAI1_RAT Guanine nucleotide-binding protein G(i) subunit alpha-1 (Gene Name=Gnai1)

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