Structure of PDB 2efe Chain D Binding Site BS01

Receptor Information
>2efe 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 IDGNH
InChIInChI=1S/C10H16N6O10P2/c11-10-14-7-4(8(19)15-10)13-2-16(7)9-6(18)5(17)3(25-9)1-24-28(22,23)26-27(12,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H3,12,20,21)(H3,11,14,15,19)/t3-,5-,6-,9-/m1/s1
InChIKeyZGPDMUBRWRJAQQ-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](N)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](N)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(N)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(N)O)O)O)N=C(NC2=O)N
FormulaC10 H16 N6 O10 P2
NameAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBL
DrugBankDB02623
ZINC
PDB chain2efe 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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PDB2efe GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system
Resolution2.08 Å
Binding residue
(original residue number in PDB)		G20 G22 K23 S24 S25 F35 N123 K124 D126 L127 S153 A154 K155
Binding residue
(residue number reindexed from 1)		G13 G15 K16 S17 S18 F28 N116 K117 D119 L120 S146 A147 K148
Annotation score3
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:2efe, PDBe:2efe, PDBj:2efe
PDBsum2efe
PubMed20833725
UniProtQ9SN68|RAF2B_ARATH Ras-related protein RABF2b (Gene Name=RABF2B)

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