Structure of PDB 5szi Chain A Binding Site BS01

Receptor Information
>5szi Chain A (length=174) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIEL
DGKRIKLQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNW
IRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSA
KANINVENAFFTLARDIKAKMDKK
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 chain5szi Chain A Residue 301 [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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PDB5szi bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		S17 G18 G20 K21 T22 C23 F33 S35 F37 S39 T40 G66 N121 K122 D124 S151 A152 K153
Binding residue
(residue number reindexed from 1)		S15 G16 G18 K19 T20 C21 F31 S33 F35 S37 T38 G64 N119 K120 D122 S149 A150 K151
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Q67
Catalytic site (residue number reindexed from 1) Q65
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0019901 protein kinase binding
GO:0031267 small GTPase binding
GO:0031489 myosin V binding
GO:1990782 protein tyrosine kinase binding
Biological Process
GO:0006887 exocytosis
GO:0006904 vesicle docking involved in exocytosis
GO:0006914 autophagy
GO:0007030 Golgi organization
GO:0007409 axonogenesis
GO:0009306 protein secretion
GO:0010506 regulation of autophagy
GO:0015031 protein transport
GO:0030030 cell projection organization
GO:0032456 endocytic recycling
GO:0032869 cellular response to insulin stimulus
GO:0032880 regulation of protein localization
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0048210 Golgi vesicle fusion to target membrane
GO:0051223 regulation of protein transport
GO:0060271 cilium assembly
GO:0061512 protein localization to cilium
GO:0072659 protein localization to plasma membrane
GO:0098887 neurotransmitter receptor transport, endosome to postsynaptic membrane
GO:0098969 neurotransmitter receptor transport to postsynaptic membrane
GO:0099003 vesicle-mediated transport in synapse
Cellular Component
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005813 centrosome
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005929 cilium
GO:0008021 synaptic vesicle
GO:0010008 endosome membrane
GO:0030140 trans-Golgi network transport vesicle
GO:0030425 dendrite
GO:0030496 midbody
GO:0030670 phagocytic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0032588 trans-Golgi network membrane
GO:0036064 ciliary basal body
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043197 dendritic spine
GO:0045202 synapse
GO:0045335 phagocytic vesicle
GO:0055037 recycling endosome
GO:0055038 recycling endosome membrane
GO:0060170 ciliary membrane
GO:0070062 extracellular exosome
GO:0097546 ciliary base
GO:0097730 non-motile cilium
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5szi, PDBe:5szi, PDBj:5szi
PDBsum5szi
PubMed27552051
UniProtP61006|RAB8A_HUMAN Ras-related protein Rab-8A (Gene Name=RAB8A)

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