Structure of PDB 5svl Chain A Binding Site BS01

Receptor Information

>5svl Chain A (length=333) Species: 9606 (Homo sapiens)

KSVVVKSWTIGIINRVVQLLIISYFVGWVFLHEKAYQVRDTAIESSVVTK
VKGSGLYANRVMDVSDYVTPPQGTSVFVIITKMIVTENQMQGFCPESEEK
YRCVSDSQCGPERLPGGGILTGRCVNYSSVLRTCEIQGWCPTEVDTVETP
IMMEAENFTIFIKNSIRFPLFNFEKGNLLPNLTARDMKTCRFHPDKDPFC
PILRVGDVVKFAGQDFAKLARTGGVLGIKIGWVCDLDKAWDQCIPKYSFT
RLDSVSEKSSVSPGYNFRFAKYYKMENGSEYRTLLKAFGIRFDVLVYGNA
GKFNIIPTIISSVAAFTSVGVGTVLCDIILLNF

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 5svl Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5svl X-ray structures define human P2X3 receptor gating cycle and antagonist action.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): V274 S275 N279 R281 K299
• Binding residue (residue number reindexed from 1): V261 S262 N266 R268 K286
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=8.55,Kd=2.8nM

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