Structure of PDB 2al7 Chain A Binding Site BS01

Receptor Information
>2al7 Chain A (length=155) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKEEMELTLVGLQYSGKTTFVNVIAVGFNMRKVTKGNVTIKIWDIGGQPR
FRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVLV
LGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWL
IQHSK
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 chain2al7 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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PDB2al7 GTP-like conformation of GDP-bound ARL10C GTPase
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Y29 S30 G31 K32 T33 T34 N129 K130 D132 L133 S162 K164
Binding residue
(residue number reindexed from 1)		Y14 S15 G16 K17 T18 T19 N103 K104 D106 L107 S136 K138
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Q74
Catalytic site (residue number reindexed from 1) Q48
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
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Biological Process
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Cellular Component
External links
PDB RCSB:2al7, PDBe:2al7, PDBj:2al7
PDBsum2al7
PubMed
UniProtQ9NVJ2|ARL8B_HUMAN ADP-ribosylation factor-like protein 8B (Gene Name=ARL8B)

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