Structure of PDB 5vdh Chain B Binding Site BS03

Receptor Information
>5vdh Chain B (length=343) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APMSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETT
MDYRVNIFLRQKWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKG
ANFHEVTTDNKLLRIFKNGNVLYSIRLTLTLSCPMDLKNFPMDVQTCIMQ
LESFGYTMNDLIFEWQDEAPVQVAEGLTLPQFLLKEEKDLRYCTKHYNTG
KFTCIEVRFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVAL
GITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVN
FVSRAGTKVFIDRAKKIDTISRACFPLAFLIFNIFYWVIYKIL
Ligand information
Ligand IDIVM
InChIInChI=1S/C48H74O14/c1-11-25(2)43-28(5)17-18-47(62-43)23-34-20-33(61-47)16-15-27(4)42(26(3)13-12-14-32-24-55-45-40(49)29(6)19-35(46(51)58-34)48(32,45)52)59-39-22-37(54-10)44(31(8)57-39)60-38-21-36(53-9)41(50)30(7)56-38/h12-15,19,25-26,28,30-31,33-45,49-50,52H,11,16-18,20-24H2,1-10H3/b13-12+,27-15+,32-14+/t25-,26-,28-,30-,31-,33+,34-,35-,36-,37-,38-,39-,40+,41-,42-,43+,44-,45+,47+,48+/m0/s1
InChIKeyAZSNMRSAGSSBNP-XPNPUAGNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC[C@H](C)[C@@H]1[C@H](CC[C@@]2(O1)C[C@@H]3C[C@H](O2)C/C=C(/[C@H]([C@H](/C=C/C=C/4\CO[C@H]5[C@@]4([C@@H](C=C([C@H]5O)C)C(=O)O3)O)C)O[C@H]6C[C@@H]([C@H]([C@@H](O6)C)O[C@H]7C[C@@H]([C@H]([C@@H](O7)C)O)OC)OC)\C)C
CACTVS 3.370CC[C@H](C)[C@H]1O[C@]2(CC[C@@H]1C)C[C@@H]3C[C@@H](C\C=C(/C)[C@@H](O[C@H]4C[C@H](OC)[C@@H](O[C@H]5C[C@H](OC)[C@@H](O)[C@H](C)O5)[C@H](C)O4)[C@@H](C)\C=C\C=C6/CO[C@@H]7[C@H](O)C(=C[C@@H](C(=O)O3)[C@]67O)C)O2
OpenEye OEToolkits 1.7.6CCC(C)C1C(CCC2(O1)CC3CC(O2)CC=C(C(C(C=CC=C4COC5C4(C(C=C(C5O)C)C(=O)O3)O)C)OC6CC(C(C(O6)C)OC7CC(C(C(O7)C)O)OC)OC)C)C
CACTVS 3.370CC[CH](C)[CH]1O[C]2(CC[CH]1C)C[CH]3C[CH](CC=C(C)[CH](O[CH]4C[CH](OC)[CH](O[CH]5C[CH](OC)[CH](O)[CH](C)O5)[CH](C)O4)[CH](C)C=CC=C6CO[CH]7[CH](O)C(=C[CH](C(=O)O3)[C]67O)C)O2
ACDLabs 12.01O=C5OC2CC(OC1(OC(C(C)CC)C(C)CC1)C2)CC=C(C)C(OC4OC(C)C(OC3OC(C)C(O)C(OC)C3)C(OC)C4)C(C=CC=C6COC7C(O)C(=CC5C67O)C)C
FormulaC48 H74 O14
Name(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside;
22,23-DIHYDROAVERMECTIN B1A;
IVERMECTIN
ChEMBLCHEMBL263291
DrugBank
ZINCZINC000252286706
PDB chain5vdh Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vdh Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		I225 Q226 I229 P230 L233
Binding residue
(residue number reindexed from 1)		I220 Q221 I224 P225 L228
Annotation score1
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:0016594 glycine binding
GO:0022824 transmitter-gated monoatomic ion channel activity
Biological Process
GO:0006811 monoatomic ion transport
GO:0034220 monoatomic ion transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vdh, PDBe:5vdh, PDBj:5vdh
PDBsum5vdh
PubMed28479061
UniProtO75311|GLRA3_HUMAN Glycine receptor subunit alpha-3 (Gene Name=GLRA3)

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