Structure of PDB 8dzt Chain B Binding Site BS01

Receptor Information
>8dzt Chain B (length=165) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDTSEELTIAGMTFTTFD
LGGGEQARRVWKNYLPAINGIVFLVDCADHSRLVESKVELNALMTDETIS
NVPILILGNKIDRTDAISEEKLREIFGLYGQTTGKGARPMEVFMCSVLKR
QGYGEGFRWLSQYID
Ligand information
Ligand IDG4P
InChIInChI=1S/C10H17N5O17P4/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(30-36(26,27)32-34(21,22)23)3(29-9)1-28-35(24,25)31-33(18,19)20/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyBUFLLCUFNHESEH-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=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)=O)[C@@H](O[P@@](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H17 N5 O17 P4
NameGUANOSINE-5',3'-TETRAPHOSPHATE;
guanosine tetraphosphate;
ppGpp
ChEMBL
DrugBankDB04022
ZINCZINC000008217069
PDB chain8dzt Chain B Residue 204 [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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PDB8dzt The alarmone ppGpp selectively inhibits the isoform A of the human small GTPase Sar1.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D34 N35 G37 K38 T39 T40 N134 K135 D137 S179 L181
Binding residue
(residue number reindexed from 1)		D21 N22 G24 K25 T26 T27 N109 K110 D112 S146 L148
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:0140785 amino acid sensor activity
Biological Process
GO:0003400 regulation of COPII vesicle coating
GO:0006886 intracellular protein transport
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0016050 vesicle organization
GO:0016192 vesicle-mediated transport
GO:0042953 lipoprotein transport
GO:0048208 COPII vesicle coating
GO:0061024 membrane organization
GO:0070863 positive regulation of protein exit from endoplasmic reticulum
GO:0090110 COPII-coated vesicle cargo loading
GO:1903432 regulation of TORC1 signaling
GO:1904262 negative regulation of TORC1 signaling
GO:1990253 cellular response to leucine starvation
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0030127 COPII vesicle coat
GO:0032580 Golgi cisterna membrane
GO:0070971 endoplasmic reticulum exit site

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dzt, PDBe:8dzt, PDBj:8dzt
PDBsum8dzt
PubMed36369712
UniProtQ9NR31|SAR1A_HUMAN Small COPII coat GTPase SAR1A (Gene Name=SAR1A)

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