Structure of PDB 4ojk Chain A Binding Site BS01

Receptor Information
>4ojk Chain A (length=174) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV
DGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERW
LKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNNLSFIETSA
LDSTNVEEAFKNILTEIYRIVSQK
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 chain4ojk Chain A 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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PDB4ojk Crystal Structure of the cGMP-dependent Protein Kinase II Leucine Zipper and Rab11b Protein Complex Reveals Molecular Details of G-kinase-specific Interactions.
Resolution2.657 Å
Binding residue
(original residue number in PDB)		G21 V22 G23 K24 S25 N26 F36 N37 L38 E39 K41 N124 K125 D127 L128 S154 L156
Binding residue
(residue number reindexed from 1)		G16 V17 G18 K19 S20 N21 F31 N32 L33 E34 K36 N119 K120 D122 L123 S149 L151
Annotation score4
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:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0031489 myosin V binding
GO:0045296 cadherin binding
Biological Process
GO:0001881 receptor recycling
GO:0015031 protein transport
GO:0032402 melanosome transport
GO:0032456 endocytic recycling
GO:0033572 transferrin transport
GO:0035773 insulin secretion involved in cellular response to glucose stimulus
GO:0044070 regulation of monoatomic anion transport
GO:0045054 constitutive secretory pathway
GO:0045055 regulated exocytosis
GO:0071468 cellular response to acidic pH
GO:0090150 establishment of protein localization to membrane
GO:0150093 amyloid-beta clearance by transcytosis
GO:2000008 regulation of protein localization to cell surface
GO:2001135 regulation of endocytic recycling
Cellular Component
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0045202 synapse
GO:0045335 phagocytic vesicle
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ojk, PDBe:4ojk, PDBj:4ojk
PDBsum4ojk
PubMed25070890
UniProtQ15907|RB11B_HUMAN Ras-related protein Rab-11B (Gene Name=RAB11B)

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