Structure of PDB 5c46 Chain F Binding Site BS01

Receptor Information
>5c46 Chain F (length=175) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV
DGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERW
LKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSA
LDSTNVEAAFQTILTEIYRIVSQKQ
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain5c46 Chain F Residue 2000 [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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PDB5c46 Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIII beta with Rab11.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		S20 G21 V22 G23 K24 S25 N26 F36 L38 S42 T43 N124 K125 D127 L128 S154 A155 L156
Binding residue
(residue number reindexed from 1)		S15 G16 V17 G18 K19 S20 N21 F31 L33 S37 T38 N119 K120 D122 L123 S149 A150 L151
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008017 microtubule binding
GO:0016787 hydrolase activity
GO:0019905 syntaxin binding
GO:0031489 myosin V binding
GO:0051959 dynein light intermediate chain binding
Biological Process
GO:0006887 exocytosis
GO:0007080 mitotic metaphase chromosome alignment
GO:0010634 positive regulation of epithelial cell migration
GO:0010796 regulation of multivesicular body size
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0030953 astral microtubule organization
GO:0031175 neuron projection development
GO:0032402 melanosome transport
GO:0032465 regulation of cytokinesis
GO:0034394 protein localization to cell surface
GO:0036258 multivesicular body assembly
GO:0043001 Golgi to plasma membrane protein transport
GO:0048227 plasma membrane to endosome transport
GO:0051650 establishment of vesicle localization
GO:0060627 regulation of vesicle-mediated transport
GO:0061502 early endosome to recycling endosome transport
GO:0061512 protein localization to cilium
GO:0071806 protein transmembrane transport
GO:0072594 establishment of protein localization to organelle
GO:0072659 protein localization to plasma membrane
GO:0090150 establishment of protein localization to membrane
GO:0090307 mitotic spindle assembly
GO:0098887 neurotransmitter receptor transport, endosome to postsynaptic membrane
GO:0150093 amyloid-beta clearance by transcytosis
GO:1902017 regulation of cilium assembly
GO:1902954 regulation of early endosome to recycling endosome transport
GO:1903438 positive regulation of mitotic cytokinetic process
GO:1904779 regulation of protein localization to centrosome
GO:1990182 exosomal secretion
GO:2001135 regulation of endocytic recycling
Cellular Component
GO:0000139 Golgi membrane
GO:0000922 spindle pole
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005771 multivesicular body
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005813 centrosome
GO:0005814 centriole
GO:0005828 kinetochore microtubule
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030133 transport vesicle
GO:0030659 cytoplasmic vesicle membrane
GO:0030666 endocytic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0032154 cleavage furrow
GO:0032588 trans-Golgi network membrane
GO:0032991 protein-containing complex
GO:0034451 centriolar satellite
GO:0043231 intracellular membrane-bounded organelle
GO:0045335 phagocytic vesicle
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome
GO:0098837 postsynaptic recycling endosome
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5c46, PDBe:5c46, PDBj:5c46
PDBsum5c46
PubMed26756197
UniProtP62491|RB11A_HUMAN Ras-related protein Rab-11A (Gene Name=RAB11A)

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