Structure of PDB 8r1a Chain E Binding Site BS02

Receptor Information
>8r1a Chain E (length=587) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYL
MNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDV
EKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRS
KSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTY
SLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQ
DEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAI
SSGDLPCMENAVLALAQIENSAAVQKAIAHYEQQMGQKVQLPTESLQELL
DLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASS
DRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKG
IQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAK
MLQEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKL
QEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKACTI
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 chain8r1a Chain E Residue 602 [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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PDB8r1a Elucidating the activation mechanism for GBP1 oligomerization
Resolution26.8 Å
Binding residue
(original residue number in PDB)		R48 T49 G50 K51 S52 Y53 L67 G68 S69 R183 D184 P241 L247 L250
Binding residue
(residue number reindexed from 1)		R44 T45 G46 K47 S48 Y49 L63 G64 S65 R179 D180 P237 L243 L246
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.1.-
3.6.5.-
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0003779 actin binding
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0004382 GDP phosphatase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0019899 enzyme binding
GO:0019955 cytokine binding
GO:0030507 spectrin binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0051879 Hsp90 protein binding
Biological Process
GO:0032703 negative regulation of interleukin-2 production
GO:0042742 defense response to bacterium
GO:0042832 defense response to protozoan
GO:0045087 innate immune response
GO:0050848 regulation of calcium-mediated signaling
GO:0050860 negative regulation of T cell receptor signaling pathway
GO:0051607 defense response to virus
GO:0051715 cytolysis in another organism
GO:0070373 negative regulation of ERK1 and ERK2 cascade
GO:0071346 cellular response to type II interferon
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor
GO:0072665 protein localization to vacuole
GO:0140639 positive regulation of pyroptotic inflammatory response
GO:0160075 non-canonical inflammasome complex assembly
GO:1900025 negative regulation of substrate adhesion-dependent cell spreading
GO:1903076 regulation of protein localization to plasma membrane
GO:1903077 negative regulation of protein localization to plasma membrane
Cellular Component
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012506 vesicle membrane
GO:0015629 actin cytoskeleton
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0106139 symbiont cell surface

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8r1a, PDBe:8r1a, PDBj:8r1a
PDBsum8r1a
PubMed38267655
UniProtP32455|GBP1_HUMAN Guanylate-binding protein 1 (Gene Name=GBP1)

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