Structure of PDB 5k13 Chain A Binding Site BS01

Receptor Information
>5k13 Chain A (length=235) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSE
LSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE
QDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLS
AICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMK
ITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLE
Ligand information
Ligand ID6Q7
InChIInChI=1S/C27H26N2O4S/c1-27(2,3)21-7-5-6-20(16-21)25-17-24(18-8-10-19(11-9-18)26(30)31)28-29(25)22-12-14-23(15-13-22)34(4,32)33/h5-17H,1-4H3,(H,30,31)
InChIKeyHPXXLUZXJROKDE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c4c(c3cc(c1cc(ccc1)C(C)(C)C)n(c2ccc(cc2)S(C)(=O)=O)n3)ccc(c4)C(O)=O
CACTVS 3.385CC(C)(C)c1cccc(c1)c2cc(nn2c3ccc(cc3)[S](C)(=O)=O)c4ccc(cc4)C(O)=O
OpenEye OEToolkits 2.0.4CC(C)(C)c1cccc(c1)c2cc(nn2c3ccc(cc3)S(=O)(=O)C)c4ccc(cc4)C(=O)O
FormulaC27 H26 N2 O4 S
Name4-{5-(3-tert-butylphenyl)-1-[4-(methylsulfonyl)phenyl]-1H-pyrazol-3-yl}benzoic acid
ChEMBLCHEMBL3815166
DrugBank
ZINCZINC000584904714
PDB chain5k13 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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PDB5k13 Identification of potent and selective retinoic acid receptor gamma (RAR gamma ) antagonists for the treatment of osteoarthritis pain using structure based drug design.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		W225 F228 S232 C235 L266 L269 I270 I273 F286 S287 G301 F302 V395 P407
Binding residue
(residue number reindexed from 1)		W45 F48 S52 C55 L86 L89 I90 I93 F106 S107 G121 F122 V215 P227
Annotation score1
Binding affinityMOAD: Ki=1.8nM
PDBbind-CN: -logKd/Ki=8.74,Ki=1.8nM
BindingDB: Ki=1.8nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0048384 retinoic acid receptor signaling pathway
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5k13, PDBe:5k13, PDBj:5k13
PDBsum5k13
PubMed27261179
UniProtP10276|RARA_HUMAN Retinoic acid receptor alpha (Gene Name=RARA)

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