Structure of PDB 5hk2 Chain A Binding Site BS01

Receptor Information
>5hk2 Chain A (length=217) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QWAVGRRWAWAALLLAVAAVLTQVVWLWLGTQSFVFQREEIAQLARQYAG
LDHELAFSRLIVELRRLHPGHVLPDEELQWVFVNAGGWMGAMCLLHASLS
EYVLLFGTALGSRGHSGRYWAEISDTIISGTFHQWREGTTKSEVFYPGET
VVHGPGEATAVEWGPNTWMVEYGRGVIPSTLAFALADTVFSTQDFLTLFY
TLRSYARGLRLELTTYL
Ligand information
Ligand ID61V
InChIInChI=1S/C19H21IN2O/c20-17-8-6-16(7-9-17)19(23)21-18-10-12-22(13-11-18)14-15-4-2-1-3-5-15/h1-9,18H,10-14H2,(H,21,23)
InChIKeyHELCSESNNDZLFM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(cc1)CN2CCC(CC2)NC(=O)c3ccc(cc3)I
CACTVS 3.385Ic1ccc(cc1)C(=O)NC2CCN(CC2)Cc3ccccc3
ACDLabs 12.01C1C(CCN(C1)Cc2ccccc2)NC(c3ccc(I)cc3)=O
FormulaC19 H21 I N2 O
NameN-(1-benzylpiperidin-4-yl)-4-iodobenzamide
ChEMBLCHEMBL50112
DrugBank
ZINCZINC000001642602
PDB chain5hk2 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5hk2 Crystal structure of the human sigma 1 receptor.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		M93 L105 F107 S117 Y120 D126 H154 E172 Y206
Binding residue
(residue number reindexed from 1)		M92 L104 F106 S116 Y119 D125 H153 E171 Y205
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.59,Ki=2.6nM
BindingDB: Ki=1.7nM
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
View graph for
Cellular Component
External links
PDB RCSB:5hk2, PDBe:5hk2, PDBj:5hk2
PDBsum5hk2
PubMed27042935
UniProtQ99720|SGMR1_HUMAN Sigma non-opioid intracellular receptor 1 (Gene Name=SIGMAR1)

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