Structure of PDB 8jc5 Chain A Binding Site BS01

Receptor Information
>8jc5 Chain A (length=164) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTI
KIWDIGGLPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDK
PQLQGIPVLVLGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEK
DNIDITLQWLIQHS
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8jc5 Chain A Residue 201 [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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PDB8jc5 Mechanistic Insights into the Interactions of Arl8b with the RUN Domains of PLEKHM1 and SKIP.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		Q29 Y30 S31 G32 K33 T34 T35 F45 S46 E47 M49 P51 T52 G74 N130 K131 D133 L134 C164 K165
Binding residue
(residue number reindexed from 1)		Q12 Y13 S14 G15 K16 T17 T18 F28 S29 E30 M32 P34 T35 G57 N113 K114 D116 L117 C147 K148
Annotation score4
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:0019003 GDP binding
GO:0043014 alpha-tubulin binding
GO:0048487 beta-tubulin binding
Biological Process
GO:0001778 plasma membrane repair
GO:0002505 antigen processing and presentation of polysaccharide antigen via MHC class II
GO:0002747 antigen processing and presentation following phagocytosis
GO:0007059 chromosome segregation
GO:0008089 anterograde axonal transport
GO:0015031 protein transport
GO:0016197 endosomal transport
GO:0032418 lysosome localization
GO:0034498 early endosome to Golgi transport
GO:0042267 natural killer cell mediated cytotoxicity
GO:0046754 viral exocytosis
GO:0051301 cell division
GO:0061909 autophagosome-lysosome fusion
GO:0090117 endosome to lysosome transport of low-density lipoprotein particle
GO:0090385 phagosome-lysosome fusion
GO:1902774 late endosome to lysosome transport
GO:1902946 protein localization to early endosome
GO:1990927 calcium ion regulated lysosome exocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0030424 axon
GO:0030496 midbody
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0042995 cell projection
GO:0045202 synapse
GO:0051233 spindle midzone
GO:0070062 extracellular exosome
GO:0101004 cytolytic granule membrane
GO:1904115 axon cytoplasm

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:8jc5, PDBe:8jc5, PDBj:8jc5
PDBsum8jc5
PubMed37775038
UniProtQ9NVJ2|ARL8B_HUMAN ADP-ribosylation factor-like protein 8B (Gene Name=ARL8B)

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