Structure of PDB 8r4d Chain A Binding Site BS01

Receptor Information
>8r4d Chain A (length=371) Species: 1097 (Chlorobaculum tepidum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVHLQEIKVHLIGDGKTSLLKQLIGLNVVTKQAPNIKGLENDDELKECLF
HFWDFGGQEIMHASHRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIV
VMNKIDENPSYNIEQKKINERFPAIENRFHRISCESIAKSLKSAVLHPDS
IYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTL
LGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTS
ALGYILNTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSFIMKYDYLPST
IIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAI
IIWYEIKKINANFTNLDVKEF
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(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[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain8r4d Chain A Residue 1201 [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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PDB8r4d Structural insights in the GTP-driven monomerization and activation of a bacterial LRRK2 homologue using allosteric nanobodies
Resolution3.88 Å
Binding residue
(original residue number in PDB)		G459 D460 G464 K465 F516 G517 C600
Binding residue
(residue number reindexed from 1)		G13 D14 G15 K16 F55 G56 C134
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005525 GTP binding
GO:0042802 identical protein binding

View graph for
Molecular Function
External links
PDB RCSB:8r4d, PDBe:8r4d, PDBj:8r4d
PDBsum8r4d
PubMed38666771
UniProtQ8KC98

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