Structure of PDB 6dk1 Chain A Binding Site BS01

Receptor Information
>6dk1 Chain A (length=212) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RWAWAALLLAVAAVLTQVVWLWLGTQSFVFQREEIAQLARQYAGLDHELA
FSRLIVELRRLHPGHVLPDEELQWVFVNAGGWMGAMCLLHASLSEYVLLF
GTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGETVVHGPG
EATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFYTLRSYA
RGLRLELTTYLF
Ligand information
Ligand IDGM4
InChIInChI=1S/C19H27NO/c1-13(2)7-9-20-10-8-19(4)14(3)18(20)11-15-5-6-16(21)12-17(15)19/h5-7,12,14,18,21H,8-11H2,1-4H3/t14-,18+,19+/m1/s1
InChIKeyVOKSWYLNZZRQPF-CCKFTAQKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1[C@@H]2Cc3ccc(O)cc3[C@@]1(C)CCN2CC=C(C)C
OpenEye OEToolkits 2.0.6C[C@@H]1[C@@H]2Cc3ccc(cc3[C@]1(CCN2CC=C(C)C)C)O
CACTVS 3.385C[CH]1[CH]2Cc3ccc(O)cc3[C]1(C)CCN2CC=C(C)C
ACDLabs 12.01C1(C)C2(c3c(CC1N(CC2)C[C@H]=C(C)C)ccc(c3)O)C
OpenEye OEToolkits 2.0.6CC1C2Cc3ccc(cc3C1(CCN2CC=C(C)C)C)O
FormulaC19 H27 N O
Name(2S,6S,11S)-6,11-dimethyl-3-(3-methylbut-2-en-1-yl)-1,2,3,4,5,6-hexahydro-2,6-methano-3-benzazocin-8-ol
ChEMBLCHEMBL60542
DrugBank
ZINCZINC000002015833
PDB chain6dk1 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6dk1 Structural basis for sigma1receptor ligand recognition.
Resolution3.12 Å
Binding residue
(original residue number in PDB)		V84 W89 Y103 F107 E172 F184 A185
Binding residue
(residue number reindexed from 1)		V77 W82 Y96 F100 E165 F177 A178
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.65,Kd=22.5nM
BindingDB: Ki=3.1nM,Kd=11.6nM,IC50=8.2nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004985 G protein-coupled opioid receptor activity
GO:0005515 protein binding
GO:0038023 signaling receptor activity
Biological Process
GO:0006869 lipid transport
GO:0007399 nervous system development
GO:0038003 G protein-coupled opioid receptor signaling pathway
GO:0043523 regulation of neuron apoptotic process
GO:0070207 protein homotrimerization
GO:0150052 regulation of postsynapse assembly
Cellular Component
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005637 nuclear inner membrane
GO:0005640 nuclear outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005811 lipid droplet
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030426 growth cone
GO:0031410 cytoplasmic vesicle
GO:0042995 cell projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0070161 anchoring junction
GO:0098794 postsynapse
GO:0098839 postsynaptic density membrane
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6dk1, PDBe:6dk1, PDBj:6dk1
PDBsum6dk1
PubMed30291362
UniProtQ99720|SGMR1_HUMAN Sigma non-opioid intracellular receptor 1 (Gene Name=SIGMAR1)

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