Structure of PDB 3o47 Chain A Binding Site BS02

Receptor Information
>3o47 Chain A (length=289) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTRKVLKEVRVQDENNVCFECGAFNPQWVSVTYGIWICLECSGRHRGLGV
HLSFVRSVTMDKWKDIELEKMKAGGNAKFREFLESQEDYDPCWSLQEKYN
SRAAALFRDKVVALAEGREWSLESWTPPQKKEMRILMVGLDAAGKTTILY
KLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGRPLWRHYFQNTQGLIF
VVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEIT
DKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRN
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 chain3o47 Chain A Residue 502 [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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PDB3o47 Crystal structure of ARFGAP1-ARF1 fusion protein
Resolution2.8 Å
Binding residue
(original residue number in PDB)		A157 G159 K160 T161 T162 N256 K257 D259 C289 A290 T291
Binding residue
(residue number reindexed from 1)		A142 G144 K145 T146 T147 N236 K237 D239 C269 A270 T271
Annotation score4
Enzymatic activity
Enzyme Commision number ?
3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019904 protein domain specific binding
Biological Process
GO:0002090 regulation of receptor internalization
GO:0006878 intracellular copper ion homeostasis
GO:0006886 intracellular protein transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0034315 regulation of Arp2/3 complex-mediated actin nucleation
GO:0060292 long-term synaptic depression
GO:0097061 dendritic spine organization
GO:0098586 cellular response to virus
GO:1990386 mitotic cleavage furrow ingression
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0012505 endomembrane system
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030017 sarcomere
GO:0031252 cell leading edge
GO:0032991 protein-containing complex
GO:0043005 neuron projection
GO:0045202 synapse
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3o47, PDBe:3o47, PDBj:3o47
PDBsum3o47
PubMed
UniProtP84077|ARF1_HUMAN ADP-ribosylation factor 1 (Gene Name=ARF1);
Q8N6T3|ARFG1_HUMAN ADP-ribosylation factor GTPase-activating protein 1 (Gene Name=ARFGAP1)

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