Structure of PDB 7mbp Chain B Binding Site BS01

Receptor Information

>7mbp Chain B (length=996) Species: 7955 (Danio rerio)

RLGDIDFTGVSRTRGKFVRVTSSTDPAEIYQILTKQWGLAPPHLVVALMG
GDEVAQLKPWLRDTLRKGLVKAAQSTGAWILTSGLRFGITKNLGQAVRDH
SLASTSPKVRVVAIGIAPWNMIQNRDLLLSAKPDHPATYPTEDLPYGAVY
SLDCNHSHFILVDEDPKRPGATGEMRVKMLKHISLQRTGYGGTGSIEIPV
LCLLVHGEPRILQKMYKNIQNSIPWLILAGSGGVADILVTLMDRGCWDAD
IVQELLINTFPDGLHSTEITSWTKLIQRILDHGHLLTVHDPEQDSELDTV
ILKALVKACKSQSQEAQDFLDELKLAVAWNRVDIAKSEIFSGDVQWSAQD
LEEVMMEALVNDKPDFVRLFVDNGVNIKQFLTYGRLQELYCSVSEKNLLH
TLLLKKNQERQAQLKFRFTFHEVSKVLKDFLDDTCKGFYQKLNLPDMDRR
CEHPWRDLFLWAILQNRQEMANYFWAMGPEAVAAALVGCKIMKEMAHLAT
EAESARSMKNAKYEQFAMDLFSECYSNSEDRAYSLLVRKTCCWSKATVLN
IATLAEAKCFFAHDGVQALLTKVWWGAMRTDTSISRLVLTFFIPPLVWTS
LIKFNPESATFIRVVLRRWNRFWSAPVTVFMGNVIMYFAFLILFSYVLLL
DFRPPPPYGPSAAEIILYFWVFTLVLEEIRQSFFTDEDMSILKKMKLYVE
DNWNKCDMVAISLFVVGLSCRMAMSTYEAGRTVLALDFMVFTLRLIHIFA
IHKQLGPKIIIVERMIKDVFFFLFFLSVWLIAYGVTTQALLHPNDPRIDW
VFRRALYRPYLHIFGQIPLEEIDAAKMPDDNCTTDVQEIILGTLPPCPNI
YANWLVILLLVIYLLVTNVLLLNLLIAMFSYTFQVVQENADIFWKFQRYN
LIVEYHSRPALAPPFIIISHITQALLSFIKDLLERELPSGLDQKLMTWET
VQKENYLAKLEHEHRESSGERLRYTSSKVQTLLRMVGGFKDQEKRM

Ligand information

• Ligand ID: YUY
• InChI: InChI=1S/C44H72O15/c1-22-7-13-44(55-20-22)23(2)33-30(59-44)16-29-27-6-5-25-15-26(8-11-42(25,3)28(27)9-12-43(29,33)4)53-14-10-24(17-45)21-54-40-38(52)36(50)39(32(19-47)57-40)58-41-37(51)35(49)34(48)31(18-46)56-41/h5,22-24,26-41,45-52H,6-21H2,1-4H3/t22-,23+,24-,26+,27-,28+,29+,30+,31-,32-,33+,34-,35+,36-,37-,38-,39-,40-,41-,42+,43+,44-/m1/s1
• InChIKey: DNENJNRTLMHVQJ-YVPDUETGSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1CCC2(C(C3C(O2)CC4C3(CCC5C4CC=C6C5(CCC(C6)OCCC(CO)COC7C(C(C(C(O7)CO)OC8C(C(C(C(O8)CO)O)O)O)O)O)C)C)C)OC1
  CACTVS 3.385: C[C@@H]1CC[C@@]2(OC1)O[C@H]3C[C@H]4[C@@H]5CC=C6C[C@H](CC[C@]6(C)[C@H]5CC[C@]4(C)[C@H]3[C@@H]2C)OCC[C@H](CO)CO[C@@H]7O[C@H](CO)[C@@H](O[C@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@H]8O)[C@H](O)[C@H]7O
  OpenEye OEToolkits 2.0.7: C[C@@H]1CC[C@@]2([C@H]([C@H]3[C@@H](O2)C[C@@H]4[C@@]3(CC[C@H]5[C@H]4CC=C6[C@@]5(CC[C@@H](C6)OCC[C@H](CO)CO[C@H]7[C@@H]([C@H]([C@@H]([C@H](O7)CO)O[C@@H]8[C@@H]([C@H]([C@@H]([C@H](O8)CO)O)O)O)O)O)C)C)C)OC1
  ACDLabs 12.01: OC1C(O)C(O)C(CO)OC1OC1C(O)C(O)C(OC1CO)OCC(CO)CCOC1CC2=CCC3C(CCC4(C)C5C(CC34)OC3(CCC(C)CO3)C5C)C2(C)CC1
  CACTVS 3.385: C[CH]1CC[C]2(OC1)O[CH]3C[CH]4[CH]5CC=C6C[CH](CC[C]6(C)[CH]5CC[C]4(C)[CH]3[CH]2C)OCC[CH](CO)CO[CH]7O[CH](CO)[CH](O[CH]8O[CH](CO)[CH](O)[CH](O)[CH]8O)[CH](O)[CH]7O
• Formula: C44 H72 O15
• Name: (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside
• PDB chain: 7mbp Chain A Residue 1503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mbp Structures of the TRPM5 channel elucidate mechanisms of activation and inhibition.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): D889 W890
• Binding residue (residue number reindexed from 1): D799 W800
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0005227 calcium-activated cation channel activity
• GO:0005262 calcium channel activity
• GO:0005509 calcium ion binding
• GO:0042802 identical protein binding
• GO:0099604 ligand-gated calcium channel activity

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0019722 calcium-mediated signaling
• GO:0034220 monoatomic ion transmembrane transport
• GO:0055085 transmembrane transport
• GO:0070588 calcium ion transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:7mbp, PDBe:7mbp, PDBj:7mbp
• PDBsum: 7mbp
• PubMed: 34168372
• UniProt: S5UH55