Structure of PDB 6jwp Chain F Binding Site BS01

Receptor Information
>6jwp Chain F (length=289) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNRKKLLLMGRSGSGKSSMRSIIFSNYSAFDTRRLGATIDVEHSHLRFLG
NMTLNLWDCGGQDVFMENYFTKQKDHIFQMVQVLIHVFDVESTEVLKDIE
IFAKALKQLRKYSPDAKIFVLLHKMDLVQLDKREELFQIMMKNLSETSSE
FGFPNLIGFPTSIWDESLYKAWSQIVCSLIPNMSNHQSNLKKFKEIMNAL
EIILFERTTFLVICSSNLDPKRFEKISNIMKNFKQSCTKLKSGFKTLILN
NNIYVSELSSNMVCFIVLKDMNIPQELVLENIKKAKEFF
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 chain6jwp Chain F Residue 401 [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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PDB6jwp Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S15 G16 S17 G18 K19 S20 S21 T35 R36 A40 T41 G63 G64 H126 K127 D129 I166
Binding residue
(residue number reindexed from 1)		S12 G13 S14 G15 K16 S17 S18 T32 R33 A37 T38 G60 G61 H123 K124 D126 I163
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
Biological Process
GO:0006360 transcription by RNA polymerase I
GO:0006383 transcription by RNA polymerase III
GO:0006817 phosphate ion transport
GO:0006995 cellular response to nitrogen starvation
GO:0009267 cellular response to starvation
GO:0010507 negative regulation of autophagy
GO:0016237 microautophagy
GO:0031509 subtelomeric heterochromatin formation
GO:0032008 positive regulation of TOR signaling
GO:0032456 endocytic recycling
GO:0034599 cellular response to oxidative stress
GO:0071230 cellular response to amino acid stimulus
GO:1903778 protein localization to vacuolar membrane
GO:1904263 positive regulation of TORC1 signaling
Cellular Component
GO:0000329 fungal-type vacuole membrane
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005770 late endosome
GO:0005773 vacuole
GO:0005774 vacuolar membrane
GO:0016020 membrane
GO:0031902 late endosome membrane
GO:0071986 Ragulator complex
GO:1990131 Gtr1-Gtr2 GTPase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6jwp, PDBe:6jwp, PDBj:6jwp
PDBsum6jwp
PubMed31579828
UniProtQ00582|RAGAB_YEAST GTP-binding protein GTR1 (Gene Name=GTR1)

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