Structure of PDB 6u9v Chain B Binding Site BS03

Receptor Information
>6u9v Chain B (length=560) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CCSWNDVFQYETNKVTRIQSVNYGTIKWILHMTVFSYVSFALMSDKLYQR
KEPLISSVHTKVKGVAEVTENVTKLVHGIFDTADYTLPLQGNSFFVMTNY
LKSEGQEQKLCPEYPSRGKQCHSDQGCIKGWMDPQSKGIQTGRCIPYDQK
RKTCEIFAWCPAEEGKEAPRPALLRSAENFTVLIKNNIDFPGHNYTTRNI
LPGMNISCTFHKTWNPQCPIFRLGDIFQEIGENFTEVAVQGGIMGIEIYW
DCNLDSWSHRCQPKYSFRRLDDKYTNESLFPGYNFRYAKYYKENGMEKRT
LIKAFGVRFDILVFGTGGKFDIIQLVVYIGSTLSYFGLATVCIDLIINTY
ASTCCRSRVYPSCKCCEPCAVNEYYYRKKCEPIVEPKPTLKYVSFVDEPH
IWMVDQQLLGKSLQDVKGQEVPRPQTDFLELSRLSRDSPDWCQCGNCLPS
QLPENRRALEELCCRRKPGQCITTSELFSKIVLSREALQLLLLYQEPLLA
LEGEAINSKLRHCAYRSYATWRFVSQDMADFAILPSCCRWKIRKEFPKTQ
GQYSGFKYPY
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain6u9v Chain B Residue 701 [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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PDB6u9v Full-Length P2X7Structures Reveal How Palmitoylation Prevents Channel Desensitization.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		R546 H547 Y550 A567 L569 R574 K583 S589
Binding residue
(residue number reindexed from 1)		R511 H512 Y515 A532 L534 R539 K548 S554
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001530 lipopolysaccharide binding
GO:0001614 purinergic nucleotide receptor activity
GO:0004931 extracellularly ATP-gated monoatomic cation channel activity
GO:0005102 signaling receptor binding
GO:0005216 monoatomic ion channel activity
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0015267 channel activity
GO:0038023 signaling receptor activity
GO:0042802 identical protein binding
GO:0043539 protein serine/threonine kinase activator activity
GO:0097110 scaffold protein binding
Biological Process
GO:0000165 MAPK cascade
GO:0000902 cell morphogenesis
GO:0001845 phagolysosome assembly
GO:0001913 T cell mediated cytotoxicity
GO:0001916 positive regulation of T cell mediated cytotoxicity
GO:0002028 regulation of sodium ion transport
GO:0006509 membrane protein ectodomain proteolysis
GO:0006649 phospholipid transfer to membrane
GO:0006811 monoatomic ion transport
GO:0006812 monoatomic cation transport
GO:0006816 calcium ion transport
GO:0006884 cell volume homeostasis
GO:0006900 vesicle budding from membrane
GO:0006954 inflammatory response
GO:0007005 mitochondrion organization
GO:0007009 plasma membrane organization
GO:0007166 cell surface receptor signaling pathway
GO:0009306 protein secretion
GO:0009410 response to xenobiotic stimulus
GO:0009612 response to mechanical stimulus
GO:0009617 response to bacterium
GO:0010043 response to zinc ion
GO:0010467 gene expression
GO:0010524 positive regulation of calcium ion transport into cytosol
GO:0010628 positive regulation of gene expression
GO:0012501 programmed cell death
GO:0014047 glutamate secretion
GO:0014049 positive regulation of glutamate secretion
GO:0014051 gamma-aminobutyric acid secretion
GO:0014054 positive regulation of gamma-aminobutyric acid secretion
GO:0014070 response to organic cyclic compound
GO:0016079 synaptic vesicle exocytosis
GO:0016485 protein processing
GO:0017121 plasma membrane phospholipid scrambling
GO:0019228 neuronal action potential
GO:0019233 sensory perception of pain
GO:0030163 protein catabolic process
GO:0030501 positive regulation of bone mineralization
GO:0032060 bleb assembly
GO:0032308 positive regulation of prostaglandin secretion
GO:0032310 prostaglandin secretion
GO:0032496 response to lipopolysaccharide
GO:0032730 positive regulation of interleukin-1 alpha production
GO:0032731 positive regulation of interleukin-1 beta production
GO:0032755 positive regulation of interleukin-6 production
GO:0032963 collagen metabolic process
GO:0033198 response to ATP
GO:0034220 monoatomic ion transmembrane transport
GO:0034405 response to fluid shear stress
GO:0034767 positive regulation of monoatomic ion transmembrane transport
GO:0035590 purinergic nucleotide receptor signaling pathway
GO:0042098 T cell proliferation
GO:0043029 T cell homeostasis
GO:0043065 positive regulation of apoptotic process
GO:0043132 NAD transport
GO:0043409 negative regulation of MAPK cascade
GO:0043410 positive regulation of MAPK cascade
GO:0045332 phospholipid translocation
GO:0045778 positive regulation of ossification
GO:0045779 negative regulation of bone resorption
GO:0045794 negative regulation of cell volume
GO:0045821 positive regulation of glycolytic process
GO:0046513 ceramide biosynthetic process
GO:0046931 pore complex assembly
GO:0048705 skeletal system morphogenesis
GO:0048873 homeostasis of number of cells within a tissue
GO:0050714 positive regulation of protein secretion
GO:0050830 defense response to Gram-positive bacterium
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051495 positive regulation of cytoskeleton organization
GO:0051592 response to calcium ion
GO:0051602 response to electrical stimulus
GO:0051649 establishment of localization in cell
GO:0051882 mitochondrial depolarization
GO:0051899 membrane depolarization
GO:0051901 positive regulation of mitochondrial depolarization
GO:0060079 excitatory postsynaptic potential
GO:0060907 positive regulation of macrophage cytokine production
GO:0070227 lymphocyte apoptotic process
GO:0070230 positive regulation of lymphocyte apoptotic process
GO:0070231 T cell apoptotic process
GO:0070234 positive regulation of T cell apoptotic process
GO:0070588 calcium ion transmembrane transport
GO:0071359 cellular response to dsRNA
GO:0071407 cellular response to organic cyclic compound
GO:0072593 reactive oxygen species metabolic process
GO:0097190 apoptotic signaling pathway
GO:0097191 extrinsic apoptotic signaling pathway
GO:0098655 monoatomic cation transmembrane transport
GO:0099161 regulation of presynaptic dense core granule exocytosis
GO:1904172 positive regulation of bleb assembly
GO:1904669 ATP export
Cellular Component
GO:0005635 nuclear envelope
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0031594 neuromuscular junction
GO:0032059 bleb
GO:0032991 protein-containing complex
GO:0043025 neuronal cell body
GO:0043195 terminal bouton
GO:0045202 synapse
GO:0098794 postsynapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6u9v, PDBe:6u9v, PDBj:6u9v
PDBsum6u9v
PubMed31587896
UniProtQ64663|P2RX7_RAT P2X purinoceptor 7 (Gene Name=P2rx7)

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