Structure of PDB 6wj2 Chain G Binding Site BS01

Receptor Information
>6wj2 Chain G (length=308) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVN
FQIWDFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITV
SKAYKVNPDMNFEVFIHKVNGLSDDHKIETQRDIHQRANDDLADAGLEKL
HLSFYLTSIYDHSIFEAFSKVVQKLIPQLPTLENLLNIFISNSGIEKAFL
FDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYGLKEDGSGSAYD
KESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRK
AIHEVFEV
Ligand information
Ligand IDL8S
InChIInChI=1S/C10H15N4O14P3S/c15-5-3(1-25-29(19,20)27-30(21,22)28-31(23,24)32)26-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H2,12,13,17,18)/t3-,5-,6+,9+/m0/s1
InChIKeyIAOZVDCRMYYKMQ-BZKDHIKHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)n2cnc3C(=O)NC(=O)Nc23
ACDLabs 12.01N2C(Nc1n(cnc1C2=O)C3C(O)C(O)C(COP(O)(=O)OP(O)(=O)OP(O)(O)=S)O3)=O
OpenEye OEToolkits 2.0.7c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)NC(=O)NC2=O
OpenEye OEToolkits 2.0.7c1nc2c(n1[C@H]3[C@@H]([C@H]([C@@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)NC(=O)NC2=O
CACTVS 3.385O[C@@H]1[C@@H](O)[C@@H](O[C@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)n2cnc3C(=O)NC(=O)Nc23
FormulaC10 H15 N4 O14 P3 S
Name9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione
ChEMBL
DrugBank
ZINC
PDB chain6wj2 Chain G Residue 500 [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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PDB6wj2 Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		R71 G73 K74 S75 T90 T96 G119 K179 N181 I220
Binding residue
(residue number reindexed from 1)		R10 G12 K13 S14 T29 T35 G58 K118 N120 I159
Annotation score2
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6wj2, PDBe:6wj2, PDBj:6wj2
PDBsum6wj2
PubMed32868926
UniProtQ9HB90|RRAGC_HUMAN Ras-related GTP-binding protein C (Gene Name=RRAGC)

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