Structure of PDB 1vg8 Chain B Binding Site BS02

Receptor Information
>1vg8 Chain B (length=179) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDR
LVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDE
FLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETS
AKEAINVEQAFQTIARNALKQETEVELYN
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 chain1vg8 Chain B Residue 2400 [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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PDB1vg8 Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S2017 G2018 V2019 G2020 K2021 T2022 S2023 F2033 N2035 Y2037 T2040 G2066 N2125 K2126 D2128 L2129 S2155 A2156 K2157
Binding residue
(residue number reindexed from 1)		S12 G13 V14 G15 K16 T17 S18 F28 N30 Y32 T35 G61 N120 K121 D123 L124 S150 A151 K152
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:0031267 small GTPase binding
GO:1905394 retromer complex binding
Biological Process
GO:0000045 autophagosome assembly
GO:0006622 protein targeting to lysosome
GO:0006914 autophagy
GO:0007174 epidermal growth factor catabolic process
GO:0008333 endosome to lysosome transport
GO:0009617 response to bacterium
GO:0015031 protein transport
GO:0016042 lipid catabolic process
GO:0019076 viral release from host cell
GO:0022615 protein to membrane docking
GO:0036466 synaptic vesicle recycling via endosome
GO:0042147 retrograde transport, endosome to Golgi
GO:0045022 early endosome to late endosome transport
GO:0045453 bone resorption
GO:0045732 positive regulation of protein catabolic process
GO:0046907 intracellular transport
GO:0048524 positive regulation of viral process
GO:0051650 establishment of vesicle localization
GO:0061724 lipophagy
GO:0090383 phagosome acidification
GO:0090385 phagosome-lysosome fusion
GO:0098943 neurotransmitter receptor transport, postsynaptic endosome to lysosome
GO:0099003 vesicle-mediated transport in synapse
GO:0099638 endosome to plasma membrane protein transport
GO:1903542 negative regulation of exosomal secretion
GO:1903543 positive regulation of exosomal secretion
Cellular Component
GO:0000421 autophagosome membrane
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005794 Golgi apparatus
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0030904 retromer complex
GO:0031902 late endosome membrane
GO:0031966 mitochondrial membrane
GO:0033162 melanosome membrane
GO:0034045 phagophore assembly site membrane
GO:0043195 terminal bouton
GO:0043231 intracellular membrane-bounded organelle
GO:0045335 phagocytic vesicle
GO:0097208 alveolar lamellar body
GO:0098588 bounding membrane of organelle
GO:0098830 presynaptic endosome
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1vg8, PDBe:1vg8, PDBj:1vg8
PDBsum1vg8
PubMed15186776
UniProtP09527|RAB7A_RAT Ras-related protein Rab-7a (Gene Name=Rab7a)

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