Structure of PDB 3cpj Chain B Binding Site BS01

Receptor Information
>3cpj Chain B (length=164) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YDLLFKIVLIGDSGVGKSNLLSRFTKNEFNMGVEFATRTLEIEGKRIKAQ
IWDTAGQERYRAITSAYYRGAVGALIVYDSKSSSYENCNHWLSELRENAD
VAVGLIGNKSDLAHLRAVPTEESKTFAQENQLLFTETSALSENVDKAFEE
LINTIYQKVPTISL
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 chain3cpj Chain B 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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PDB3cpj A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		G23 G25 K26 S27 N28 F38 N39 M40 N126 K127 D129 L130 A157 L158
Binding residue
(residue number reindexed from 1)		G14 G16 K17 S18 N19 F29 N30 M31 N108 K109 D111 L112 A139 L140
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=4.72,Kd=18.9uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0006887 exocytosis
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0034498 early endosome to Golgi transport
Cellular Component
GO:0000139 Golgi membrane
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0016020 membrane
GO:0055037 recycling endosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3cpj, PDBe:3cpj, PDBj:3cpj
PDBsum3cpj
PubMed18426803
UniProtP38555|YPT31_YEAST GTP-binding protein YPT31/YPT8 (Gene Name=YPT31)

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