Structure of PDB 5szk Chain B Binding Site BS02

Receptor Information
>5szk Chain B (length=173) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAKTYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTI
ELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVK
QWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEFADSLGIPFLET
SAKNATNVEQAFMTMAAEIKKRM
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 chain5szk Chain B Residue 302 [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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PDB5szk bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S17 G18 G20 K21 S22 C23 Y33 E35 Y37 S39 T40 G66 N121 K122 D124 S151 A152 K153
Binding residue
(residue number reindexed from 1)		S17 G18 G20 K21 S22 C23 Y33 E35 Y37 S39 T40 G66 N121 K122 D124 S151 A152 K153
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Q67
Catalytic site (residue number reindexed from 1) Q67
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
Biological Process
GO:0000045 autophagosome assembly
GO:0006886 intracellular protein transport
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
GO:0006914 autophagy
GO:0007030 Golgi organization
GO:0015031 protein transport
GO:0019068 virion assembly
GO:0090557 establishment of endothelial intestinal barrier
GO:1903020 positive regulation of glycoprotein metabolic process
GO:2000785 regulation of autophagosome assembly
Cellular Component
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0012505 endomembrane system
GO:0016020 membrane
GO:0030133 transport vesicle
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0034045 phagophore assembly site membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5szk, PDBe:5szk, PDBj:5szk
PDBsum5szk
PubMed27552051
UniProtQ9H0U4|RAB1B_HUMAN Ras-related protein Rab-1B (Gene Name=RAB1B)

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