Structure of PDB 6y7g Chain B Binding Site BS01

Receptor Information
>6y7g Chain B (length=165) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFDYMFKLLIIGNSSVGKTSFLFRYADDSFTGIDFKVKTVFKNEKRIKLQ
IWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYS
WDNAQVILVGNKCDMEDERVISTERGQHLGEQLGFEFFETSAKDNINVKQ
TFERLVDIICDKMSE
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 chain6y7g Chain B Residue 301 [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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PDB6y7g Structure of the human RAB3C in complex with GDP
Resolution2.3 Å
Binding residue
(original residue number in PDB)		S40 G42 K43 T44 S45 N143 K144 D146 M147 S173 K175
Binding residue
(residue number reindexed from 1)		S15 G17 K18 T19 S20 N111 K112 D114 M115 S141 K143
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0030742 GTP-dependent protein binding
GO:0031489 myosin V binding
Biological Process
GO:0006887 exocytosis
GO:0009306 protein secretion
GO:0015031 protein transport
GO:0017157 regulation of exocytosis
GO:0019882 antigen processing and presentation
Cellular Component
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0030672 synaptic vesicle membrane
GO:0031982 vesicle
GO:0048471 perinuclear region of cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6y7g, PDBe:6y7g, PDBj:6y7g
PDBsum6y7g
PubMed
UniProtQ96E17|RAB3C_HUMAN Ras-related protein Rab-3C (Gene Name=RAB3C)

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