Structure of PDB 2f9m Chain A Binding Site BS02

Receptor Information
>2f9m Chain A (length=182) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVD
GKTIKAQIWDTAGQERYRRITSAYYRGAVGALLVYDIAKHLTYENVERWL
KELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNNLSFIETSAL
DSTNVEEAFKNILTEIYRIVSQKQIADRAAHD
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain2f9m Chain A Residue 1200 [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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PDB2f9m The crystal structure of the small GTPase Rab11b reveals critical differences relative to the Rab11a isoform.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		S20 G21 G23 K24 S25 N26 F36 N37 L38 S40 S42 T43 A68 G69 N124 K125 D127 L128 S154 A155 L156
Binding residue
(residue number reindexed from 1)		S14 G15 G17 K18 S19 N20 F30 N31 L32 S34 S36 T37 A62 G63 N118 K119 D121 L122 S148 A149 L150
Annotation score3
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
View graph for
Cellular Component
External links
PDB RCSB:2f9m, PDBe:2f9m, PDBj:2f9m
PDBsum2f9m
PubMed16545962
UniProtQ15907|RB11B_HUMAN Ras-related protein Rab-11B (Gene Name=RAB11B)

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