Structure of PDB 1rrg Chain B Binding Site BS01

Receptor Information
>1rrg Chain B (length=177) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGF
NVETVEYKNISFTVWDVGGIRPLWRHYFQNTQGLIFVVDSNDRERVNEAR
EELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWY
IQATCATSGDGLYEGLDWLSNQLRNQK
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 chain1rrg Chain B Residue 183 [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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PDB1rrg The structure of rat ADP-ribosylation factor-1 (ARF-1) complexed to GDP determined from two different crystal forms.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A27 G29 K30 T31 T32 N126 K127 D129 C159 A160
Binding residue
(residue number reindexed from 1)		A26 G28 K29 T30 T31 N122 K123 D125 C155 A156
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0019904 protein domain specific binding
GO:1990583 phospholipase D activator activity
Biological Process
GO:0002090 regulation of receptor internalization
GO:0006878 intracellular copper ion homeostasis
GO:0006886 intracellular protein transport
GO:0007015 actin filament organization
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0034315 regulation of Arp2/3 complex-mediated actin nucleation
GO:0034379 very-low-density lipoprotein particle assembly
GO:0045807 positive regulation of endocytosis
GO:0045956 positive regulation of calcium ion-dependent exocytosis
GO:0050714 positive regulation of protein secretion
GO:0055108 Golgi to transport vesicle transport
GO:0060292 long-term synaptic depression
GO:0060999 positive regulation of dendritic spine development
GO:0070142 synaptic vesicle budding
GO:0097061 dendritic spine organization
GO:0097212 lysosomal membrane organization
GO:0098974 postsynaptic actin cytoskeleton organization
GO:1902307 positive regulation of sodium ion transmembrane transport
GO:1902824 positive regulation of late endosome to lysosome transport
GO:1902953 positive regulation of ER to Golgi vesicle-mediated transport
GO:1903725 regulation of phospholipid metabolic process
GO:1990386 mitotic cleavage furrow ingression
Cellular Component
GO:0000139 Golgi membrane
GO:0005770 late endosome
GO:0005778 peroxisomal membrane
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0012505 endomembrane system
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030017 sarcomere
GO:0030137 COPI-coated vesicle
GO:0031252 cell leading edge
GO:0032991 protein-containing complex
GO:0043005 neuron projection
GO:0045202 synapse
GO:0098978 glutamatergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1rrg, PDBe:1rrg, PDBj:1rrg
PDBsum1rrg
PubMed7552752
UniProtP84079|ARF1_RAT ADP-ribosylation factor 1 (Gene Name=Arf1)

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