Structure of PDB 3cph Chain A Binding Site BS01

Receptor Information
>3cph Chain A (length=175) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKV
KLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVN
EHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNV
NEIFFTLAKLIQEKIDSNKLVGVGN
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 chain3cph Chain A Residue 302 [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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PDB3cph A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		S29 G30 V31 G32 K33 S34 C35 F45 F49 N133 K134 D136 M137 S162 A163 K164
Binding residue
(residue number reindexed from 1)		S10 G11 V12 G13 K14 S15 C16 F26 F30 N114 K115 D117 M118 S143 A144 K145
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=6.48,Kd=0.33uM
Enzymatic activity
Catalytic site (original residue number in PDB) Q79
Catalytic site (residue number reindexed from 1) Q60
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:0006893 Golgi to plasma membrane transport
GO:0006906 vesicle fusion
GO:0006914 autophagy
GO:0007107 membrane addition at site of cytokinesis
GO:0009306 protein secretion
GO:0015031 protein transport
GO:0031321 ascospore-type prospore assembly
Cellular Component
GO:0000131 incipient cellular bud site
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0005935 cellular bud neck
GO:0030133 transport vesicle
GO:0030658 transport vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0043332 mating projection tip

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3cph, PDBe:3cph, PDBj:3cph
PDBsum3cph
PubMed18426803
UniProtP07560|SEC4_YEAST Ras-related protein SEC4 (Gene Name=SEC4)

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