Structure of PDB 6mne Chain B Binding Site BS02

Receptor Information
>6mne Chain B (length=278) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKTQGRLWEAAR
ALACPPGSLETLQLDVRDSKSVAAARERVTEGRVDVLVCNAGLGLLGPLE
ALGEDAVASVLDVNVVGTVRMLQAFLPDMKRRGSGRVLVTGSVGGLMGLP
FNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTGSPEEVLDRT
DIHTFHRFYQYLAHSKQVFREAAQNPEEVAEVFLTALRAPKPTLRYFTTE
RFLPLLRMRLDDPSGSNYVTAMHREVFG
Ligand information
Ligand IDJ3Z
InChIInChI=1S/C18H22O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-16,19H,2,4,6-9H2,1H3/t14-,15-,16+,18+/m1/s1
InChIKeyDNXHEGUUPJUMQT-CBZIJGRNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CCC2=O)O
CACTVS 3.352C[C@]12CC[C@H]3[C@@H](CCc4cc(O)ccc34)[C@@H]1CCC2=O
CACTVS 3.352C[C]12CC[CH]3[CH](CCc4cc(O)ccc34)[CH]1CCC2=O
OpenEye OEToolkits 1.6.1CC12CCC3c4ccc(cc4CCC3C1CCC2=O)O
FormulaC18 H22 O2
Name(9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one;
Estrone
ChEMBLCHEMBL1405
DrugBankDB00655
ZINCZINC000013509425
PDB chain6mne Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6mne Crystal structures of human 17 beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NADP+reveal the mechanism of substrate inhibition.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		Y155 H221 F226 F259
Binding residue
(residue number reindexed from 1)		Y155 H214 F219 F252
Annotation score5
Binding affinityMOAD: Kd=1.6uM
BindingDB: IC50=810nM,Ki=3nM
Enzymatic activity
Enzyme Commision number 1.1.1.51: 3(or 17)beta-hydroxysteroid dehydrogenase.
1.1.1.62: 17beta-estradiol 17-dehydrogenase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004303 estradiol 17-beta-dehydrogenase [NAD(P)+] activity
GO:0005496 steroid binding
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0030283 testosterone dehydrogenase [NAD(P)+] activity
GO:0036094 small molecule binding
GO:0042803 protein homodimerization activity
GO:0047035 testosterone dehydrogenase (NAD+) activity
GO:0047045 testosterone 17-beta-dehydrogenase (NADP+) activity
GO:0050661 NADP binding
GO:0070401 NADP+ binding
GO:0072582 17-beta-hydroxysteroid dehydrogenase (NADP+) activity
GO:1903924 estradiol binding
Biological Process
GO:0006629 lipid metabolic process
GO:0006694 steroid biosynthetic process
GO:0006703 estrogen biosynthetic process
GO:0007040 lysosome organization
GO:0007519 skeletal muscle tissue development
GO:0008210 estrogen metabolic process
GO:0010467 gene expression
GO:0060348 bone development
GO:0060612 adipose tissue development
GO:0061370 testosterone biosynthetic process
GO:0071248 cellular response to metal ion
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6mne, PDBe:6mne, PDBj:6mne
PDBsum6mne
PubMed30768851
UniProtP14061|DHB1_HUMAN 17-beta-hydroxysteroid dehydrogenase type 1 (Gene Name=HSD17B1)

[Back to BioLiP]