Structure of PDB 4o9s Chain A Binding Site BS01

Receptor Information
>4o9s Chain A (length=175) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDET
GQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKG
NDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQK
IVRQRQEELCLARQYRLIVHNGYCD
Ligand information
Ligand ID2RY
InChIInChI=1S/C22H21F3N4OS/c23-22(24,25)16-6-2-1-4-14(16)12-18(30)28-8-10-29(11-9-28)20-19-15-5-3-7-17(15)31-21(19)27-13-26-20/h1-2,4,6,13H,3,5,7-12H2
InChIKeyXMIMIFRXLOGETC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385FC(F)(F)c1ccccc1CC(=O)N2CCN(CC2)c3ncnc4sc5CCCc5c34
OpenEye OEToolkits 2.0.7c1ccc(c(c1)CC(=O)N2CCN(CC2)c3c4c5c(sc4ncn3)CCC5)C(F)(F)F
FormulaC22 H21 F3 N4 O S
Name1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone
ChEMBLCHEMBL3288147
DrugBank
ZINCZINC000169348410
PDB chain4o9s Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4o9s Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		L35 F36 L37 A55 A57 M73 G75 M88 Y90 Y133 F135
Binding residue
(residue number reindexed from 1)		L35 F36 L37 A55 A57 M73 G75 M88 Y90 Y133 F135
Annotation score1
Binding affinityMOAD: ic50=0.28uM
PDBbind-CN: -logKd/Ki=6.55,IC50=0.28uM
BindingDB: IC50=60nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005501 retinoid binding
GO:0005515 protein binding
GO:0016918 retinal binding
GO:0019841 retinol binding
GO:0034632 retinol transmembrane transporter activity
Biological Process
GO:0001654 eye development
GO:0002639 positive regulation of immunoglobulin production
GO:0006094 gluconeogenesis
GO:0007507 heart development
GO:0007601 visual perception
GO:0030277 maintenance of gastrointestinal epithelium
GO:0030324 lung development
GO:0032024 positive regulation of insulin secretion
GO:0032526 response to retinoic acid
GO:0034633 retinol transport
GO:0042572 retinol metabolic process
GO:0042593 glucose homeostasis
GO:0048562 embryonic organ morphogenesis
GO:0048706 embryonic skeletal system development
GO:0048738 cardiac muscle tissue development
GO:0048807 female genitalia morphogenesis
GO:0060044 negative regulation of cardiac muscle cell proliferation
GO:0060059 embryonic retina morphogenesis in camera-type eye
GO:0060065 uterus development
GO:0060068 vagina development
GO:0060157 urinary bladder development
GO:0060347 heart trabecula formation
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4o9s, PDBe:4o9s, PDBj:4o9s
PDBsum4o9s
PubMed24835984
UniProtP02753|RET4_HUMAN Retinol-binding protein 4 (Gene Name=RBP4)

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