Structure of PDB 7t3c Chain D Binding Site BS01

Receptor Information
>7t3c Chain D (length=296) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLG
NLVLNLWDCGGQDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMH
YYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRP
LECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVL
LFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEV
RNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
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 chain7t3c Chain D Residue 501 [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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PDB7t3c Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		G17 S18 G19 K20 T21 S22 R37 T42 H127 K128 D130 I164
Binding residue
(residue number reindexed from 1)		G13 S14 G15 K16 T17 S18 R33 T38 H123 K124 D126 I160
Annotation score4
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:0031625 ubiquitin protein ligase binding
GO:0042803 protein homodimerization activity
GO:0043495 protein-membrane adaptor activity
GO:0046982 protein heterodimerization activity
GO:0051219 phosphoprotein binding
Biological Process
GO:0006915 apoptotic process
GO:0008104 protein localization
GO:0009267 cellular response to starvation
GO:0010507 negative regulation of autophagy
GO:0031669 cellular response to nutrient levels
GO:0032008 positive regulation of TOR signaling
GO:0033209 tumor necrosis factor-mediated signaling pathway
GO:0034198 cellular response to amino acid starvation
GO:0035556 intracellular signal transduction
GO:0042593 glucose homeostasis
GO:0061462 protein localization to lysosome
GO:0071230 cellular response to amino acid stimulus
GO:0072657 protein localization to membrane
GO:1904263 positive regulation of TORC1 signaling
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0016020 membrane
GO:1990130 GATOR1 complex
GO:1990131 Gtr1-Gtr2 GTPase complex
GO:1990877 FNIP-folliculin RagC/D GAP

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7t3c, PDBe:7t3c, PDBj:7t3c
PDBsum7t3c
PubMed35338845
UniProtQ7L523|RRAGA_HUMAN Ras-related GTP-binding protein A (Gene Name=RRAGA)

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