Structure of PDB 7t3c Chain E Binding Site BS01

Receptor Information
>7t3c Chain E (length=306) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRILLMGLRRSGKSSIQKVVFHKMSPNETLALESTNKIYKDDISNSSFVN
FQIWDFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITV
SKAYKVNPDMNFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKL
HLSFYLTSIYDHSIFEAFSKVVQKLIPQLPTLENLLNIFISNSGIEKAFL
FDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYGLKEDGSGSAYD
KESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRK
AIHEVF
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 E Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		R71 S72 G73 K74 S76 L91 L93 E94 S95 K179 D181 S219 I220
Binding residue
(residue number reindexed from 1)		R10 S11 G12 K13 S15 L30 L32 E33 S34 K118 D120 S158 I159
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0043495 protein-membrane adaptor activity
GO:0046982 protein heterodimerization activity
GO:0051020 GTPase binding
GO:0060090 molecular adaptor activity
GO:0140767 enzyme-substrate adaptor activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0006915 apoptotic process
GO:0007264 small GTPase-mediated signal transduction
GO:0008104 protein localization
GO:0008380 RNA splicing
GO:0009267 cellular response to starvation
GO:0010507 negative regulation of autophagy
GO:0031669 cellular response to nutrient levels
GO:0032006 regulation of TOR signaling
GO:0034198 cellular response to amino acid starvation
GO:0043200 response to amino acid
GO:0061462 protein localization to lysosome
GO:0071230 cellular response to amino acid stimulus
GO:0072657 protein localization to membrane
GO:1903432 regulation of TORC1 signaling
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:0043231 intracellular membrane-bounded organelle
GO:1990131 Gtr1-Gtr2 GTPase complex
GO:1990877 FNIP-folliculin RagC/D GAP

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7t3c, PDBe:7t3c, PDBj:7t3c
PDBsum7t3c
PubMed35338845
UniProtQ9HB90|RRAGC_HUMAN Ras-related GTP-binding protein C (Gene Name=RRAGC)

[Back to BioLiP]