Structure

Physi-Chem Properties

Molecular Weight:  270.18
Volume:  283.408
LogP:  1.742
LogD:  1.912
LogS:  -2.204
# Rotatable Bonds:  1
TPSA:  69.92
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.627
Synthetic Accessibility Score:  5.45
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.792
MDCK Permeability:  8.28419069875963e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.037
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.152
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.19
Plasma Protein Binding (PPB):  57.19170379638672%
Volume Distribution (VD):  1.164
Pgp-substrate:  38.50166702270508%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.122
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.774
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.125
CYP3A4-inhibitor:  0.019
CYP3A4-substrate:  0.237

ADMET: Excretion

Clearance (CL):  7.518
Half-life (T1/2):  0.614

ADMET: Toxicity

hERG Blockers:  0.037
Human Hepatotoxicity (H-HT):  0.26
Drug-inuced Liver Injury (DILI):  0.28
AMES Toxicity:  0.146
Rat Oral Acute Toxicity:  0.374
Maximum Recommended Daily Dose:  0.034
Skin Sensitization:  0.09
Carcinogencity:  0.287
Eye Corrosion:  0.004
Eye Irritation:  0.046
Respiratory Toxicity:  0.849

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC143576

Natural Product ID:  NPC143576
Common Name*:   (1S,2S,3R,6R,7R,8S)-8-Isopropyl-1-Methyl-5-Methylene-11-Oxabicyclo[4.4.1]Undecane-2,3,7-Triol
IUPAC Name:   (1R,4R,5S,6S,9S,10R)-6-methyl-2-methylidene-9-propan-2-yl-11-oxabicyclo[4.4.1]undecane-4,5,10-triol
Synonyms:  
Standard InCHIKey:  PXMMQRQCUPJJQX-ZYIYBEKCSA-N
Standard InCHI:  InChI=1S/C15H26O4/c1-8(2)10-5-6-15(4)14(18)11(16)7-9(3)13(19-15)12(10)17/h8,10-14,16-18H,3,5-7H2,1-2,4H3/t10-,11+,12+,13+,14-,15-/m0/s1
SMILES:  C=C1C[C@@H](O)[C@@H]([C@]2(O[C@H]1[C@H](O)[C@@H](CC2)C(C)C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL457585
PubChem CID:   44583978
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane sesquiterpenoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO29822 Santolina insularis Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[15974607]
NPO29822 Santolina insularis Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[15974607]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT492 Cell Line Caco-2 Homo sapiens IC50 = 3700.0 nM PMID[509942]
NPT27 Others Unspecified IC50 >= 10.0 ug.mL-1 PMID[509942]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC143576 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7949 Intermediate Similarity NPC476701
0.7821 Intermediate Similarity NPC477089
0.7792 Intermediate Similarity NPC170148
0.7792 Intermediate Similarity NPC293223
0.7662 Intermediate Similarity NPC36479
0.7639 Intermediate Similarity NPC250836
0.7564 Intermediate Similarity NPC329626
0.7561 Intermediate Similarity NPC231601
0.7532 Intermediate Similarity NPC190859
0.7468 Intermediate Similarity NPC476703
0.7439 Intermediate Similarity NPC103171
0.7403 Intermediate Similarity NPC476709
0.7349 Intermediate Similarity NPC471340
0.7342 Intermediate Similarity NPC236228
0.7342 Intermediate Similarity NPC256720
0.7317 Intermediate Similarity NPC118116
0.7308 Intermediate Similarity NPC471525
0.7294 Intermediate Similarity NPC476217
0.7294 Intermediate Similarity NPC475019
0.7294 Intermediate Similarity NPC474949
0.7284 Intermediate Similarity NPC86971
0.7262 Intermediate Similarity NPC83702
0.72 Intermediate Similarity NPC33583
0.72 Intermediate Similarity NPC161612
0.72 Intermediate Similarity NPC163290
0.7195 Intermediate Similarity NPC76054
0.7176 Intermediate Similarity NPC329749
0.7176 Intermediate Similarity NPC471379
0.7176 Intermediate Similarity NPC290731
0.7176 Intermediate Similarity NPC196911
0.7162 Intermediate Similarity NPC471200
0.716 Intermediate Similarity NPC52755
0.7143 Intermediate Similarity NPC260852
0.7143 Intermediate Similarity NPC239308
0.7126 Intermediate Similarity NPC476723
0.7126 Intermediate Similarity NPC476724
0.7123 Intermediate Similarity NPC50435
0.7108 Intermediate Similarity NPC474894
0.7108 Intermediate Similarity NPC77003
0.7108 Intermediate Similarity NPC5361
0.7093 Intermediate Similarity NPC474762
0.7093 Intermediate Similarity NPC255143
0.7093 Intermediate Similarity NPC476015
0.7079 Intermediate Similarity NPC122057
0.7067 Intermediate Similarity NPC311736
0.7045 Intermediate Similarity NPC97103
0.7045 Intermediate Similarity NPC115607
0.7045 Intermediate Similarity NPC49783
0.7045 Intermediate Similarity NPC299527
0.7042 Intermediate Similarity NPC41180
0.7042 Intermediate Similarity NPC152438
0.7037 Intermediate Similarity NPC471454
0.7033 Intermediate Similarity NPC220221
0.7013 Intermediate Similarity NPC16964
0.7013 Intermediate Similarity NPC472947
0.7011 Intermediate Similarity NPC190753
0.7011 Intermediate Similarity NPC248602
0.7011 Intermediate Similarity NPC186148
0.7 Intermediate Similarity NPC24443
0.6988 Remote Similarity NPC474592
0.6988 Remote Similarity NPC474739
0.6986 Remote Similarity NPC475807
0.6986 Remote Similarity NPC172622
0.6966 Remote Similarity NPC206614
0.6966 Remote Similarity NPC474323
0.6957 Remote Similarity NPC476009
0.6951 Remote Similarity NPC264610
0.6951 Remote Similarity NPC475980
0.6941 Remote Similarity NPC5958
0.6932 Remote Similarity NPC248312
0.6932 Remote Similarity NPC177629
0.6932 Remote Similarity NPC153805
0.6932 Remote Similarity NPC281516
0.6932 Remote Similarity NPC58219
0.6923 Remote Similarity NPC470041
0.6923 Remote Similarity NPC129630
0.6923 Remote Similarity NPC471781
0.6905 Remote Similarity NPC246621
0.6897 Remote Similarity NPC475684
0.6897 Remote Similarity NPC470242
0.6897 Remote Similarity NPC311163
0.6889 Remote Similarity NPC329952
0.6889 Remote Similarity NPC70251
0.6889 Remote Similarity NPC184463
0.6889 Remote Similarity NPC475881
0.6883 Remote Similarity NPC305698
0.6882 Remote Similarity NPC474313
0.6882 Remote Similarity NPC471150
0.686 Remote Similarity NPC474780
0.6854 Remote Similarity NPC215556
0.6854 Remote Similarity NPC473564
0.6854 Remote Similarity NPC133450
0.6854 Remote Similarity NPC92974
0.6854 Remote Similarity NPC173926
0.6849 Remote Similarity NPC475412
0.6848 Remote Similarity NPC476720
0.6848 Remote Similarity NPC475900
0.6848 Remote Similarity NPC472873
0.6842 Remote Similarity NPC469328
0.6842 Remote Similarity NPC267027
0.6835 Remote Similarity NPC306085
0.6829 Remote Similarity NPC84360
0.6824 Remote Similarity NPC477390
0.6824 Remote Similarity NPC477385
0.6818 Remote Similarity NPC189777
0.6818 Remote Similarity NPC44538
0.6813 Remote Similarity NPC474792
0.6813 Remote Similarity NPC470187
0.6813 Remote Similarity NPC67398
0.6813 Remote Similarity NPC91654
0.6813 Remote Similarity NPC475788
0.6813 Remote Similarity NPC474835
0.6813 Remote Similarity NPC475912
0.6813 Remote Similarity NPC212486
0.68 Remote Similarity NPC476702
0.6795 Remote Similarity NPC304690
0.6795 Remote Similarity NPC74722
0.6795 Remote Similarity NPC234511
0.679 Remote Similarity NPC12696
0.679 Remote Similarity NPC93213
0.6786 Remote Similarity NPC100697
0.6782 Remote Similarity NPC298595
0.6782 Remote Similarity NPC47958
0.6782 Remote Similarity NPC149725
0.6782 Remote Similarity NPC304509
0.6782 Remote Similarity NPC471494
0.6782 Remote Similarity NPC476725
0.6778 Remote Similarity NPC3952
0.6778 Remote Similarity NPC216284
0.6778 Remote Similarity NPC312471
0.6778 Remote Similarity NPC471378
0.6778 Remote Similarity NPC177668
0.6778 Remote Similarity NPC470832
0.6778 Remote Similarity NPC197107
0.6753 Remote Similarity NPC73603
0.6753 Remote Similarity NPC82337
0.6753 Remote Similarity NPC259299
0.675 Remote Similarity NPC95165
0.675 Remote Similarity NPC477085
0.6747 Remote Similarity NPC68119
0.6747 Remote Similarity NPC3852
0.6747 Remote Similarity NPC13823
0.6744 Remote Similarity NPC127917
0.6744 Remote Similarity NPC128246
0.6742 Remote Similarity NPC217983
0.6742 Remote Similarity NPC470260
0.6742 Remote Similarity NPC207114
0.6742 Remote Similarity NPC79549
0.6742 Remote Similarity NPC22376
0.6742 Remote Similarity NPC75443
0.6742 Remote Similarity NPC227379
0.6742 Remote Similarity NPC474471
0.6742 Remote Similarity NPC92370
0.6742 Remote Similarity NPC202672
0.6742 Remote Similarity NPC309656
0.6739 Remote Similarity NPC473258
0.6739 Remote Similarity NPC190294
0.6737 Remote Similarity NPC471381
0.6737 Remote Similarity NPC70865
0.6705 Remote Similarity NPC322922
0.6705 Remote Similarity NPC187661
0.6705 Remote Similarity NPC472379
0.6705 Remote Similarity NPC321812
0.6705 Remote Similarity NPC281316
0.6705 Remote Similarity NPC470836
0.6703 Remote Similarity NPC12172
0.6703 Remote Similarity NPC158061
0.6703 Remote Similarity NPC8729
0.6703 Remote Similarity NPC184063
0.6703 Remote Similarity NPC210268
0.6703 Remote Similarity NPC208886
0.6703 Remote Similarity NPC131209
0.6703 Remote Similarity NPC30515
0.6702 Remote Similarity NPC304445
0.6702 Remote Similarity NPC26307
0.6702 Remote Similarity NPC311904
0.6702 Remote Similarity NPC181151
0.6702 Remote Similarity NPC236580
0.6667 Remote Similarity NPC233295
0.6667 Remote Similarity NPC93869
0.6667 Remote Similarity NPC160517
0.6667 Remote Similarity NPC475963
0.6667 Remote Similarity NPC78673
0.6667 Remote Similarity NPC197447
0.6667 Remote Similarity NPC155935
0.6667 Remote Similarity NPC474776
0.6667 Remote Similarity NPC186155
0.6667 Remote Similarity NPC6765
0.6667 Remote Similarity NPC36954
0.6667 Remote Similarity NPC473508
0.6667 Remote Similarity NPC291875
0.6667 Remote Similarity NPC307411
0.6667 Remote Similarity NPC14961
0.6667 Remote Similarity NPC474951
0.6667 Remote Similarity NPC270013
0.6667 Remote Similarity NPC151176
0.6667 Remote Similarity NPC3464
0.6667 Remote Similarity NPC272961
0.6667 Remote Similarity NPC266578
0.6667 Remote Similarity NPC469583

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC143576 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6778 Remote Similarity NPD7838 Discovery
0.6629 Remote Similarity NPD7524 Approved
0.6593 Remote Similarity NPD46 Approved
0.6593 Remote Similarity NPD6698 Approved
0.6495 Remote Similarity NPD5344 Discontinued
0.6477 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6364 Remote Similarity NPD6695 Phase 3
0.6364 Remote Similarity NPD371 Approved
0.6311 Remote Similarity NPD6371 Approved
0.6176 Remote Similarity NPD7899 Clinical (unspecified phase)
0.617 Remote Similarity NPD7983 Approved
0.6104 Remote Similarity NPD368 Approved
0.6087 Remote Similarity NPD7750 Discontinued
0.6064 Remote Similarity NPD3168 Discontinued
0.6061 Remote Similarity NPD6648 Approved
0.6023 Remote Similarity NPD6930 Phase 2
0.6023 Remote Similarity NPD6931 Approved
0.5974 Remote Similarity NPD1145 Discontinued
0.596 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5957 Remote Similarity NPD1695 Approved
0.593 Remote Similarity NPD6933 Approved
0.5909 Remote Similarity NPD6929 Approved
0.5882 Remote Similarity NPD1811 Approved
0.5882 Remote Similarity NPD1810 Approved
0.587 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5833 Remote Similarity NPD7087 Discontinued
0.5816 Remote Similarity NPD1698 Clinical (unspecified phase)
0.581 Remote Similarity NPD6686 Approved
0.5806 Remote Similarity NPD4249 Approved
0.58 Remote Similarity NPD4225 Approved
0.5794 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5745 Remote Similarity NPD4250 Approved
0.5745 Remote Similarity NPD4251 Approved
0.5741 Remote Similarity NPD6053 Discontinued
0.5714 Remote Similarity NPD5282 Discontinued
0.5714 Remote Similarity NPD7532 Clinical (unspecified phase)
0.5699 Remote Similarity NPD6893 Approved
0.5699 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5698 Remote Similarity NPD6924 Approved
0.5698 Remote Similarity NPD6926 Approved
0.5688 Remote Similarity NPD8133 Approved
0.5682 Remote Similarity NPD5776 Phase 2
0.5682 Remote Similarity NPD6932 Approved
0.5682 Remote Similarity NPD6925 Approved
0.5667 Remote Similarity NPD7514 Phase 3
0.5667 Remote Similarity NPD4821 Approved
0.5667 Remote Similarity NPD4820 Approved
0.5667 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5667 Remote Similarity NPD4822 Approved
0.5667 Remote Similarity NPD4819 Approved
0.5667 Remote Similarity NPD7332 Phase 2
0.566 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5619 Remote Similarity NPD6640 Phase 3
0.5618 Remote Similarity NPD7145 Approved
0.5612 Remote Similarity NPD5779 Approved
0.5612 Remote Similarity NPD5778 Approved
0.5607 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5604 Remote Similarity NPD6898 Phase 1

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data