Structure of PDB 1ukv Chain Y Binding Site BS01

Receptor Information
>1ukv Chain Y (length=197) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEYDYLFKLLLIGNSGVGKSCLLLRFSDDTYTNDYISTIGVDFKIKTVEL
DGKTVKLQIWDTAGQERFRTITSSYYRGSHGIIIVYDVTDQESFNGVKMW
LQEIDRYATSTVLKLLVGNKCDLKDKRVVEYDVAKEFADANKMPFLETSA
LDSTNVEDAFLTMARQIKESMSQQNLNETTQKKEDKGNVNLKGQSLC
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 chain1ukv Chain Y Residue 1207 [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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PDB1ukv Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase
Resolution1.5 Å
Binding residue
(original residue number in PDB)		G18 V19 G20 K21 S22 C23 Y33 D36 Y37 N121 K122 D124 L125 S151 L153
Binding residue
(residue number reindexed from 1)		G16 V17 G18 K19 S20 C21 Y31 D34 Y35 N119 K120 D122 L123 S149 L151
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000149 SNARE binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0000045 autophagosome assembly
GO:0006886 intracellular protein transport
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0016236 macroautophagy
GO:0032258 cytoplasm to vacuole targeting by the Cvt pathway
GO:0032456 endocytic recycling
GO:0034497 protein localization to phagophore assembly site
GO:0034498 early endosome to Golgi transport
GO:0035493 SNARE complex assembly
GO:0035494 SNARE complex disassembly
GO:0048194 Golgi vesicle budding
GO:0048211 Golgi vesicle docking
GO:0061709 reticulophagy
GO:0090114 COPII-coated vesicle budding
GO:1900101 regulation of endoplasmic reticulum unfolded protein response
GO:1990261 pre-mRNA catabolic process
Cellular Component
GO:0000139 Golgi membrane
GO:0000407 phagophore assembly site
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0005801 cis-Golgi network
GO:0005829 cytosol
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0031410 cytoplasmic vesicle
GO:0034045 phagophore assembly site membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ukv, PDBe:1ukv, PDBj:1ukv
PDBsum1ukv
PubMed14576435
UniProtP01123|YPT1_YEAST GTP-binding protein YPT1 (Gene Name=YPT1)

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