Structure of PDB 6fx0 Chain A Binding Site BS01

Receptor Information
>6fx0 Chain A (length=238) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YELSPQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDK
FSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRY
TPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETG
LLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRM
LMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE
Ligand information
Ligand IDE9T
InChIInChI=1S/C27H26O3/c28-25-6-5-22(20-1-2-21-11-23(26(29)30)4-3-19(21)10-20)12-24(25)27-13-16-7-17(14-27)9-18(8-16)15-27/h1-6,10-12,16-18,28H,7-9,13-15H2,(H,29,30)/t16-,17+,18-,27-
InChIKeyLDGIHZJOIQSHPB-HYVKCOOLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(cc2c1cc(cc2)C(=O)O)c3ccc(c(c3)C45CC6CC(C4)CC(C6)C5)O
CACTVS 3.385OC(=O)c1ccc2cc(ccc2c1)c3ccc(O)c(c3)C45CC6CC(CC(C6)C4)C5
FormulaC27 H26 O3
Name6-[3-(1-adamantyl)-4-oxidanyl-phenyl]naphthalene-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6fx0 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fx0 Structure-based design of Trifarotene (CD5789), a potent and selective RAR gamma agonist for the treatment of acne.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F230 A234 C237 L268 L271 R278 F288 S289 F304
Binding residue
(residue number reindexed from 1)		F51 A55 C58 L89 L92 R99 F109 S110 F125
Annotation score1
Binding affinityBindingDB: Ki=77nM,EC50=49nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 DNA-binding transcription factor activity
GO:0004879 nuclear receptor activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
GO:0046965 nuclear retinoid X receptor binding
GO:1990837 sequence-specific double-stranded DNA binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001843 neural tube closure
GO:0002063 chondrocyte development
GO:0002068 glandular epithelial cell development
GO:0003417 growth plate cartilage development
GO:0003430 growth plate cartilage chondrocyte growth
GO:0006355 regulation of DNA-templated transcription
GO:0006915 apoptotic process
GO:0008283 cell population proliferation
GO:0008284 positive regulation of cell population proliferation
GO:0008285 negative regulation of cell population proliferation
GO:0008361 regulation of cell size
GO:0009755 hormone-mediated signaling pathway
GO:0009952 anterior/posterior pattern specification
GO:0010468 regulation of gene expression
GO:0010628 positive regulation of gene expression
GO:0012501 programmed cell death
GO:0030154 cell differentiation
GO:0031076 embryonic camera-type eye development
GO:0031641 regulation of myelination
GO:0032331 negative regulation of chondrocyte differentiation
GO:0032526 response to retinoic acid
GO:0035116 embryonic hindlimb morphogenesis
GO:0035264 multicellular organism growth
GO:0043065 positive regulation of apoptotic process
GO:0043068 positive regulation of programmed cell death
GO:0045596 negative regulation of cell differentiation
GO:0045637 regulation of myeloid cell differentiation
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048048 embryonic eye morphogenesis
GO:0048384 retinoic acid receptor signaling pathway
GO:0048608 reproductive structure development
GO:0048732 gland development
GO:0060070 canonical Wnt signaling pathway
GO:0060173 limb development
GO:0060324 face development
GO:0060348 bone development
GO:0060349 bone morphogenesis
GO:0060429 epithelium development
GO:0060534 trachea cartilage development
GO:0060740 prostate gland epithelium morphogenesis
GO:0061037 negative regulation of cartilage development
GO:0070384 Harderian gland development
GO:0071300 cellular response to retinoic acid
GO:0072089 stem cell proliferation
GO:1990830 cellular response to leukemia inhibitory factor
GO:2000647 negative regulation of stem cell proliferation
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005737 cytoplasm
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:6fx0, PDBe:6fx0, PDBj:6fx0
PDBsum6fx0
PubMed29706423
UniProtP13631|RARG_HUMAN Retinoic acid receptor gamma (Gene Name=RARG)

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