Structure of PDB 7lpd Chain D Binding Site BS02

Receptor Information
>7lpd Chain D (length=497) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALHIAIERRNMTLVTLLVEGFYFGELPLSLAACTNQLAIVKFLLQNSARD
SVGNTVLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNR
KGLTPLALAASSGKIGVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSL
YDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVK
RIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILS
VSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYF
SQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFM
FVYLVFLFGFSTAVVTLIEDSYNSLYSTCLELFKFTIGMGDLEFTENYDF
KAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITI
LDTEKSFLKCMRKAFRSGKLLQVGFTPDGKDDYRWCFRVDEVNWTTW
Ligand information
Ligand ID4DY
InChIInChI=1S/C18H27NO3/c1-14(2)8-6-4-5-7-9-18(21)19-13-15-10-11-16(20)17(12-15)22-3/h6,8,10-12,14,20H,4-5,7,9,13H2,1-3H3,(H,19,21)/b8-6+
InChIKeyYKPUWZUDDOIDPM-SOFGYWHQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)/C=C/CCCCC(=O)NCc1ccc(c(c1)OC)O
CACTVS 3.385COc1cc(CNC(=O)CCCCC=CC(C)C)ccc1O
ACDLabs 12.01c1(CNC(CCCC[C@H]=CC(C)C)=O)cc(OC)c(cc1)O
CACTVS 3.385COc1cc(CNC(=O)CCCC/C=C/C(C)C)ccc1O
OpenEye OEToolkits 1.7.6CC(C)C=CCCCCC(=O)NCc1ccc(c(c1)OC)O
FormulaC18 H27 N O3
Name(6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide;
Capsaicin;
8-Methyl-N-vanillyl-trans-6-nonenamide;
NGX-4010
ChEMBLCHEMBL294199
DrugBankDB06774
ZINCZINC000001530575
PDB chain7lpd Chain D Residue 903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7lpd Heat-dependent opening of TRPV1 in the presence of capsaicin.
Resolution3.55 Å
Binding residue
(original residue number in PDB)		Y511 S512 L515 F543 T550 N551
Binding residue
(residue number reindexed from 1)		Y280 S281 L284 F312 T319 N320
Annotation score1
Binding affinityBindingDB: EC50=300nM,Ki=2000nM,IC50=19nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004888 transmembrane signaling receptor activity
GO:0005216 monoatomic ion channel activity
GO:0005230 extracellular ligand-gated monoatomic ion channel activity
GO:0005231 excitatory extracellular ligand-gated monoatomic ion channel activity
GO:0005261 monoatomic cation channel activity
GO:0005262 calcium channel activity
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005524 ATP binding
GO:0008289 lipid binding
GO:0008324 monoatomic cation transmembrane transporter activity
GO:0015276 ligand-gated monoatomic ion channel activity
GO:0015278 intracellularly gated calcium channel activity
GO:0017081 chloride channel regulator activity
GO:0035091 phosphatidylinositol binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0051219 phosphoprotein binding
GO:0097603 temperature-gated ion channel activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001659 temperature homeostasis
GO:0001660 fever generation
GO:0001774 microglial cell activation
GO:0002024 diet induced thermogenesis
GO:0002790 peptide secretion
GO:0003085 negative regulation of systemic arterial blood pressure
GO:0006629 lipid metabolic process
GO:0006811 monoatomic ion transport
GO:0006816 calcium ion transport
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0009268 response to pH
GO:0009408 response to heat
GO:0010459 negative regulation of heart rate
GO:0010917 negative regulation of mitochondrial membrane potential
GO:0014047 glutamate secretion
GO:0014832 urinary bladder smooth muscle contraction
GO:0019233 sensory perception of pain
GO:0019722 calcium-mediated signaling
GO:0034220 monoatomic ion transmembrane transport
GO:0034605 cellular response to heat
GO:0043065 positive regulation of apoptotic process
GO:0043434 response to peptide hormone
GO:0045429 positive regulation of nitric oxide biosynthetic process
GO:0048265 response to pain
GO:0048266 behavioral response to pain
GO:0050909 sensory perception of taste
GO:0050954 sensory perception of mechanical stimulus
GO:0050955 thermoception
GO:0050960 detection of temperature stimulus involved in thermoception
GO:0050965 detection of temperature stimulus involved in sensory perception of pain
GO:0050968 detection of chemical stimulus involved in sensory perception of pain
GO:0051289 protein homotetramerization
GO:0055085 transmembrane transport
GO:0060079 excitatory postsynaptic potential
GO:0060083 smooth muscle contraction involved in micturition
GO:0070588 calcium ion transmembrane transport
GO:0071312 cellular response to alkaloid
GO:0071318 cellular response to ATP
GO:0071345 cellular response to cytokine stimulus
GO:0071356 cellular response to tumor necrosis factor
GO:0071363 cellular response to growth factor stimulus
GO:0071468 cellular response to acidic pH
GO:0071502 cellular response to temperature stimulus
GO:0090212 negative regulation of establishment of blood-brain barrier
GO:0098703 calcium ion import across plasma membrane
GO:1901594 response to capsazepine
GO:1990090 cellular response to nerve growth factor stimulus
Cellular Component
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0030425 dendrite
GO:0032591 dendritic spine membrane
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0098982 GABA-ergic synapse

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7lpd, PDBe:7lpd, PDBj:7lpd
PDBsum7lpd
PubMed34239123
UniProtO35433|TRPV1_RAT Transient receptor potential cation channel subfamily V member 1 (Gene Name=Trpv1)

[Back to BioLiP]