Structure of PDB 2efc Chain D Binding Site BS01

Receptor Information
>2efc Chain D (length=165) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDA
TVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQE
LQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTA
TNVKEIFYEIARRLP
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 chain2efc Chain D Residue 2200 [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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PDB2efc GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system
Resolution2.09 Å
Binding residue
(original residue number in PDB)		V19 G20 G22 K23 S24 S25 F35 N123 K124 D126 L127 S153 K155
Binding residue
(residue number reindexed from 1)		V12 G13 G15 K16 S17 S18 F28 N116 K117 D119 L120 S146 K148
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0036094 small molecule binding
GO:0140313 molecular sequestering activity
Biological Process
GO:0006886 intracellular protein transport
GO:0007033 vacuole organization
GO:0015031 protein transport
GO:0045324 late endosome to vacuole transport
Cellular Component
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0031901 early endosome membrane
GO:0032585 multivesicular body membrane
GO:0043229 intracellular organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2efc, PDBe:2efc, PDBj:2efc
PDBsum2efc
PubMed20833725
UniProtQ9SN68|RAF2B_ARATH Ras-related protein RABF2b (Gene Name=RABF2B)

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