Structure of PDB 3d7m Chain A Binding Site BS03

Receptor Information

>3d7m Chain A (length=305) Species: 10116 (Rattus norvegicus)

VKLLLLGAGESGKSTIVKQMKICHEAGYSEEECKQYKAVVYSNTIQSIIA
IIRAMGRLKIDFGDAARADDARQLFVLAAELAGVIKRLWKDSGVQACFNR
SREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFK
DLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNR
MHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAG
SNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVCFVFDAVTDV
IIKNN

Ligand information

• Ligand ID: GDP
• InChI: InChI=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
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=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 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(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
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 3d7m Chain A Residue 355

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d7m Helix dipole movement and conformational variability contribute to allosteric GDP release in Galphai subunits.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): E43 S44 G45 K46 S47 T48 S151 R176 T177 R178 N269 K270 D272 L273 C325 A326
• Binding residue (residue number reindexed from 1): E10 S11 G12 K13 S14 T15 S109 R134 T135 R136 N227 K228 D230 L231 C283 A284
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=6.44,Kd=0.36uM

Enzymatic activity

• Catalytic site (original residue number in PDB): E43 T48 R178 D200 Q204
• Catalytic site (residue number reindexed from 1): E10 T15 R136 D158 Q162

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

External links

• PDB: RCSB:3d7m, PDBe:3d7m, PDBj:3d7m
• PDBsum: 3d7m
• PubMed: 19222191
• UniProt: P10824|GNAI1_RAT Guanine nucleotide-binding protein G(i) subunit alpha-1 (Gene Name=Gnai1)