Structure of PDB 1m13 Chain A Binding Site BS01

Receptor Information
>1m13 Chain A (length=273) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVKWSQVRKDLCSLKV
SLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVI
SYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDT
AGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRV
VDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRL
LRIQDIHPFATPLMQELFGITGS
Ligand information
Ligand IDHYF
InChIInChI=1S/C35H52O4/c1-22(2)13-12-19-33(11)27(16-14-23(3)4)21-34(20-18-25(7)8)30(37)28(17-15-24(5)6)31(38)35(33,32(34)39)29(36)26(9)10/h13-15,18,26-27,38H,12,16-17,19-21H2,1-11H3/t27-,33-,34-,35+/m1/s1
InChIKeyIWBJJCOKGLUQIZ-OJCNYLSASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C(=O)C12C(=C(C(=O)C(C1=O)(CC(C2(C)CCC=C(C)C)CC=C(C)C)CC=C(C)C)CC=C(C)C)O
OpenEye OEToolkits 1.5.0CC(C)C(=O)[C@]12C(=C(C(=O)[C@](C1=O)(C[C@H]([C@@]2(C)CCC=C(C)C)CC=C(C)C)CC=C(C)C)CC=C(C)C)O
CACTVS 3.341CC(C)C(=O)[C]12C(=C(CC=C(C)C)C(=O)[C](CC=C(C)C)(C[CH](CC=C(C)C)[C]1(C)CCC=C(C)C)C2=O)O
CACTVS 3.341CC(C)C(=O)[C@@]12C(=C(CC=C(C)C)C(=O)[C@@](CC=C(C)C)(C[C@@H](CC=C(C)C)[C@@]1(C)CCC=C(C)C)C2=O)O
ACDLabs 10.04O=C1C2(C(O)=C(C(=O)C1(CC(C\C=C(/C)C)C2(C)CC\C=C(/C)C)C\C=C(/C)C)C\C=C(/C)C)C(=O)C(C)C
FormulaC35 H52 O4
Name4-HYDROXY-5-ISOBUTYRYL-6-METHYL-1,3,7-TRIS-(3-METHYL-BUT-2-ENYL)-6-(4-METHYL-PENT-3-ENYL)-BICYCLO[3.3.1]NON-3-ENE-2,9-DIONE;
HYPERFORIN
ChEMBL
DrugBank
ZINCZINC000014514079
PDB chain1m13 Chain A Residue 435 [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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PDB1m13 2.1 A Crystal Structure of Human PXR in Complex with the St. John's Wort Compound Hyperforin
Resolution2.15 Å
Binding residue
(original residue number in PDB)		L209 M243 S247 F281 C284 Q285 F288 W299 M323 H407 I414
Binding residue
(residue number reindexed from 1)		L48 M82 S86 F120 C123 Q124 F127 W138 M162 H246 I253
Annotation score1
Binding affinityMOAD: Kd=27nM
PDBbind-CN: -logKd/Ki=7.57,Kd=27nM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1m13, PDBe:1m13, PDBj:1m13
PDBsum1m13
PubMed12578355
UniProtO75469|NR1I2_HUMAN Nuclear receptor subfamily 1 group I member 2 (Gene Name=NR1I2)

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