Structure

Physi-Chem Properties

Molecular Weight:  298.25
Volume:  340.982
LogP:  4.118
LogD:  3.459
LogS:  -3.847
# Rotatable Bonds:  15
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.285
Synthetic Accessibility Score:  2.859
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.764
MDCK Permeability:  4.7235524107236415e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.405
Plasma Protein Binding (PPB):  95.84394073486328%
Volume Distribution (VD):  1.169
Pgp-substrate:  3.3954296112060547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.312
CYP1A2-substrate:  0.291
CYP2C19-inhibitor:  0.185
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.234
CYP2C9-substrate:  0.802
CYP2D6-inhibitor:  0.072
CYP2D6-substrate:  0.113
CYP3A4-inhibitor:  0.491
CYP3A4-substrate:  0.128

ADMET: Excretion

Clearance (CL):  4.569
Half-life (T1/2):  0.874

ADMET: Toxicity

hERG Blockers:  0.052
Human Hepatotoxicity (H-HT):  0.307
Drug-inuced Liver Injury (DILI):  0.084
AMES Toxicity:  0.068
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.754
Skin Sensitization:  0.962
Carcinogencity:  0.344
Eye Corrosion:  0.916
Eye Irritation:  0.959
Respiratory Toxicity:  0.327

Download Data

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

  Natural Product: NPC185885

Natural Product ID:  NPC185885
Common Name*:   WMDVSLKCVMKCRK-VIFPVBQESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WMDVSLKCVMKCRK-VIFPVBQESA-N
Standard InCHI:  InChI=1S/C17H20O3/c1-9-6-5-7-13-14(9)11(3)15-10(2)8-19-17(15)16(13)20-12(4)18/h8-9H,5-7H2,1-4H3/t9-/m0/s1
SMILES:  C[C@H]1CCCc2c1c(C)c1c(C)coc1c2OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14431892
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0003655] Eremophilane, 8,9-secoeremophilane and furoeremophilane 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
NPO25807 Psacalium decompositum Species n.a. n.a. n.a. n.a. n.a. PMID[10479309]
NPO25807 Psacalium decompositum Species n.a. n.a. n.a. n.a. n.a. PMID[32672964]
NPO28508 Flourensia cernua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28034 Artemisia sylvatica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28034 Artemisia sylvatica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28508 Flourensia cernua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28034 Artemisia sylvatica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28508 Flourensia cernua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25807 Psacalium decompositum Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23760 Scytonema hofmannii Species Scytonemataceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28317 Marinobacter hydrocarbonoclasticus Species Alteromonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20198 Lobaria isidiosa Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT113 Cell Line RAW264.7 Mus musculus FC = 2.5 n.a. PMID[32672964]
NPT113 Cell Line RAW264.7 Mus musculus FC = 2.0 n.a. PMID[32672964]
NPT3087 Individual Protein Transcription factor p65 Mus musculus FC = 0.2 n.a. PMID[32672964]
NPT2 Others Unspecified FC = 1.7 n.a. PMID[32672964]
NPT2 Others Unspecified FC = 2.1 n.a. PMID[32672964]
NPT32 Organism Mus musculus Mus musculus Activity = 6.56 mg PMID[32672964]
NPT32 Organism Mus musculus Mus musculus Inhibition = 70.3 % PMID[32672964]
NPT27358 SINGLE PROTEIN Inhibitor of nuclear factor kappa-B kinase subunit alpha Mus musculus FC = 3.2 n.a. PMID[32672964]

☑ 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 NPC185885 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

  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 NPC185885 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

  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