Structure of PDB 5svm Chain A Binding Site BS01

Receptor Information

>5svm Chain A (length=323) Species: 9606 (Homo sapiens)

GIINRVVQLLIISYFVGWVFLHEKAYQVRDTAIESSVVTKVKGSGLYANR
VMDVSDYVTPPQGTSVFVIITKMIVTENQMQGFCPESEEKYRCVSDSQCG
PERLPGGGILTGRCVNYSSVLRTCEIQGWCPTEVDTVETPIMMEAENFTI
FIKNSIRFPLFNFEKGNLLPNLTARDMKTCRFHPDKDPFCPILRVGDVVK
FAGQDFAKLARTGGVLGIKIGWVCDLDKAWDQCIPKYSFTRLDSVSEKSS
VSPGYNFRFAKYYKMENGSEYRTLLKAFGIRFDVLVYGNAGKFNIIPTII
SSVAAFTSVGVGTVLCDIILLNF

Ligand information

• Ligand ID: 6AT
• InChI: InChI=1S/C11H18N5O13P3S/c1-33-11-14-8(12)5-9(15-11)16(3-13-5)10-7(18)6(17)4(27-10)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-4,6-7,10,17-18H,2H2,1H3,(H,22,23)(H,24,25)(H2,12,14,15)(H2,19,20,21)/t4-,6-,7-,10-/m1/s1
• InChIKey: XNOBOKJVOTYSJV-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CSc1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.385: CSc1nc(N)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)c2n1
  OpenEye OEToolkits 1.7.6: CSc1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.385: CSc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(nc(SC)nc12)N)C(O)C3O
• Formula: C11 H18 N5 O13 P3 S
• Name: 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate);
  2-methylthio-adenosine-5'-triphosphate
• ChEMBL: CHEMBL336208
• ZINC: ZINC000003995334
• PDB chain: 5svm Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5svm X-ray structures define human P2X3 receptor gating cycle and antagonist action.
• Resolution: 3.093 Å
• Binding residue (original residue number in PDB): V274 S275 N279 R281 K299
• Binding residue (residue number reindexed from 1): V251 S252 N256 R258 K276
• Annotation score: 1
• Binding affinity: BindingDB: Ki=8.2nM,EC50=350nM

Gene Ontology

Molecular Function

• GO:0001614 purinergic nucleotide receptor activity
• GO:0004931 extracellularly ATP-gated monoatomic cation channel activity
• GO:0005216 monoatomic ion channel activity
• GO:0005524 ATP binding
• GO:0015267 channel activity

Biological Process

• GO:0001666 response to hypoxia
• GO:0006811 monoatomic ion transport
• GO:0006812 monoatomic cation transport
• GO:0007165 signal transduction
• GO:0007268 chemical synaptic transmission
• GO:0007274 neuromuscular synaptic transmission
• GO:0009266 response to temperature stimulus
• GO:0009408 response to heat
• GO:0009409 response to cold
• GO:0009612 response to mechanical stimulus
• GO:0009743 response to carbohydrate
• GO:0010524 positive regulation of calcium ion transport into cytosol
• GO:0014832 urinary bladder smooth muscle contraction
• GO:0030432 peristalsis
• GO:0033198 response to ATP
• GO:0034220 monoatomic ion transmembrane transport
• GO:0035590 purinergic nucleotide receptor signaling pathway
• GO:0048167 regulation of synaptic plasticity
• GO:0048266 behavioral response to pain
• GO:0050804 modulation of chemical synaptic transmission
• GO:0050850 positive regulation of calcium-mediated signaling
• GO:0050909 sensory perception of taste
• GO:0051649 establishment of localization in cell
• GO:0060079 excitatory postsynaptic potential
• GO:0070207 protein homotrimerization
• GO:0070588 calcium ion transmembrane transport
• GO:0071318 cellular response to ATP
• GO:0098655 monoatomic cation transmembrane transport
• GO:0098662 inorganic cation transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0030424 axon
• GO:0043005 neuron projection
• GO:0043235 receptor complex
• GO:0098685 Schaffer collateral - CA1 synapse
• GO:0098686 hippocampal mossy fiber to CA3 synapse
• GO:0098794 postsynapse

External links

• PDB: RCSB:5svm, PDBe:5svm, PDBj:5svm
• PDBsum: 5svm
• PubMed: 27626375
• UniProt: P56373|P2RX3_HUMAN P2X purinoceptor 3 (Gene Name=P2RX3)