Structure of PDB 3x1x Chain A Binding Site BS01

Receptor Information
>3x1x Chain A (length=166) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQ
CMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQI
LRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWSNCAFLESSAKS
KINVNEIFYDLVRQIN
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 chain3x1x Chain A Residue 201 [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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PDB3x1x The structure and conformational switching of Rap1B
Resolution1.0 Å
Binding residue
(original residue number in PDB)		G13 G15 K16 S17 A18 F28 E30 G60 N116 K117 D119 L120 S147 A148 K149
Binding residue
(residue number reindexed from 1)		G13 G15 K16 S17 A18 F28 E30 G60 N116 K117 D119 L120 S147 A148 K149
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.5.2: small monomeric GTPase.
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003925 G protein activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0019003 GDP binding
GO:0044877 protein-containing complex binding
Biological Process
GO:0007165 signal transduction
GO:0007264 small GTPase-mediated signal transduction
GO:0008283 cell population proliferation
GO:0009743 response to carbohydrate
GO:0017156 calcium-ion regulated exocytosis
GO:0030033 microvillus assembly
GO:0032486 Rap protein signal transduction
GO:0033625 positive regulation of integrin activation
GO:0045955 negative regulation of calcium ion-dependent exocytosis
GO:0051649 establishment of localization in cell
GO:0061028 establishment of endothelial barrier
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071320 cellular response to cAMP
GO:0071407 cellular response to organic cyclic compound
GO:0071466 cellular response to xenobiotic stimulus
GO:0097211 cellular response to gonadotropin-releasing hormone
GO:0099010 modification of postsynaptic structure
GO:1901888 regulation of cell junction assembly
GO:2000114 regulation of establishment of cell polarity
GO:2000301 negative regulation of synaptic vesicle exocytosis
Cellular Component
GO:0005737 cytoplasm
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0045121 membrane raft
GO:0070161 anchoring junction
GO:0098978 glutamatergic synapse

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3x1x, PDBe:3x1x, PDBj:3x1x
PDBsum3x1x
PubMed25935485
UniProtQ62636|RAP1B_RAT Ras-related protein Rap-1b (Gene Name=Rap1b)

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