Structure of PDB 5di3 Chain A Binding Site BS01

Receptor Information
>5di3 Chain A (length=164) Species: 3055 (Chlamydomonas reinhardtii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EARILVLGLDNAGKTTILKALSEEDITTITPTQGFNIKSLSRDGFNLKIW
DIGGQKSIRPYWRNYFDQTDALIYVIDSADSKRLSESEFELTELLQEEKM
TGVPLLVFANKQDLVGALAADEIASTLDLTSIRDRPWQIQACSAKQGTGL
KEGMEWMMKQVKLE
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)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)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain5di3 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5di3 A G-protein activation cascade from Arl13B to Arl3 and implications for ciliary targeting of lipidated proteins.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D25 N26 G28 K29 T30 T31 P46 T47 G68 G69 N125 K126 D128 L129 S158 A159 K160
Binding residue
(residue number reindexed from 1)		D10 N11 G13 K14 T15 T16 P31 T32 G53 G54 N110 K111 D113 L114 S143 A144 K145
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) D85
Catalytic site (residue number reindexed from 1) D70
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0015031 protein transport
GO:0051301 cell division
Cellular Component
GO:0000139 Golgi membrane
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005815 microtubule organizing center
GO:0005819 spindle
GO:0005856 cytoskeleton
GO:0016020 membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5di3, PDBe:5di3, PDBj:5di3
PDBsum5di3
PubMed26551564
UniProtA8ISN6|ARL3_CHLRE ADP-ribosylation factor-like protein 3 (Gene Name=ARL3)

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