Structure of PDB 5di3 Chain B Binding Site BS01

Receptor Information
>5di3 Chain B (length=204) Species: 3055 (Chlamydomonas reinhardtii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRKITIALLGLDNAGKTTLLNSIQGEVDRDTTPTFGFNSTTLNEGKYKIE
VFDLGGGKNIRGVWKKYLAEVHAIVYVVDAADPGRFEESKMTMAEVLENQ
FMRDKPICIFANKQDLPTAAPAAEVVKGLGLATCRNSHNVFPCTAKMPAG
QDVDHRLRDGLKWLVGTVDREFGRLDPRVQTEAEEVRQEEARKKKEREER
LRKQ
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 B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		D28 N29 G31 K32 T33 T34 T47 T50 N128 K129 D131 L132 T160 A161 K162
Binding residue
(residue number reindexed from 1)		D12 N13 G15 K16 T17 T18 T31 T34 N112 K113 D115 L116 T144 A145 K146
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L58
Catalytic site (residue number reindexed from 1) L42
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005525 GTP binding

View graph for
Molecular Function
External links
PDB RCSB:5di3, PDBe:5di3, PDBj:5di3
PDBsum5di3
PubMed26551564
UniProtA8INQ0|ARL13_CHLRE ADP-ribosylation factor-like protein 13B (Gene Name=ARL13)

[Back to BioLiP]