Structure of PDB 8jpb Chain Q Binding Site BS01

Receptor Information

>8jpb Chain Q (length=317) Species: 9606 (Homo sapiens)

RELKLLLLGTGESGKSTFIKQMRIIHGSGYSDEDKRGFTKLVYQNIFTAM
QAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENPYVDAIKSLWN
DPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPTT
GIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQ
VLVESDNENRMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSH
LVDYFPEYDGPQRDAQAAREFILKMFVDLNPDSDKIIYSHFTCATDTENI
RFVFAAVKDTILQLNLK

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: 8jpb Chain Q Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8jpb GPCR activation and GRK2 assembly by a biased intracellular agonist.
• Resolution: 3.07 Å
• Binding residue (original residue number in PDB): E49 G51 K52 S53 T54 D155 R181 V182 R183 N274 K275 D277 L278 C330 A331 T332
• Binding residue (residue number reindexed from 1): E12 G14 K15 S16 T17 D118 R144 V145 R146 N237 K238 D240 L241 C293 A294 T295
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0001664 G protein-coupled receptor binding
• GO:0003924 GTPase activity
• GO:0003925 G protein activity
• GO:0005096 GTPase activator activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019001 guanyl nucleotide binding
• GO:0030234 enzyme regulator activity
• GO:0031683 G-protein beta/gamma-subunit complex binding
• GO:0046872 metal ion binding

Biological Process

• GO:0001508 action potential
• GO:0006469 negative regulation of protein kinase activity
• GO:0007165 signal transduction
• GO:0007186 G protein-coupled receptor signaling pathway
• GO:0007189 adenylate cyclase-activating G protein-coupled receptor signaling pathway
• GO:0007200 phospholipase C-activating G protein-coupled receptor signaling pathway
• GO:0007206 phospholipase C-activating G protein-coupled glutamate receptor signaling pathway
• GO:0007208 phospholipase C-activating serotonin receptor signaling pathway
• GO:0007213 G protein-coupled acetylcholine receptor signaling pathway
• GO:0007215 glutamate receptor signaling pathway
• GO:0007218 neuropeptide signaling pathway
• GO:0007596 blood coagulation
• GO:0007603 phototransduction, visible light
• GO:0009649 entrainment of circadian clock
• GO:0010543 regulation of platelet activation
• GO:0034695 response to prostaglandin E
• GO:0050821 protein stabilization
• GO:0060158 phospholipase C-activating dopamine receptor signaling pathway
• GO:0060828 regulation of canonical Wnt signaling pathway

Cellular Component

• GO:0001750 photoreceptor outer segment
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005765 lysosomal membrane
• GO:0005794 Golgi apparatus
• GO:0005834 heterotrimeric G-protein complex
• GO:0005886 plasma membrane
• GO:0031965 nuclear membrane
• GO:0045202 synapse
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:8jpb, PDBe:8jpb, PDBj:8jpb
• PDBsum: 8jpb
• PubMed: 37532940
• UniProt: P50148|GNAQ_HUMAN Guanine nucleotide-binding protein G(q) subunit alpha (Gene Name=GNAQ)