Structure

Physi-Chem Properties

Molecular Weight:  338.15
Volume:  360.172
LogP:  5.548
LogD:  3.359
LogS:  -4.056
# Rotatable Bonds:  3
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.801
Synthetic Accessibility Score:  3.162
Fsp3:  0.286
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.733
MDCK Permeability:  1.931057522597257e-05
Pgp-inhibitor:  0.629
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.009

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.091
Plasma Protein Binding (PPB):  98.19054412841797%
Volume Distribution (VD):  0.893
Pgp-substrate:  3.479335069656372%

ADMET: Metabolism

CYP1A2-inhibitor:  0.362
CYP1A2-substrate:  0.664
CYP2C19-inhibitor:  0.911
CYP2C19-substrate:  0.387
CYP2C9-inhibitor:  0.91
CYP2C9-substrate:  0.933
CYP2D6-inhibitor:  0.529
CYP2D6-substrate:  0.363
CYP3A4-inhibitor:  0.372
CYP3A4-substrate:  0.222

ADMET: Excretion

Clearance (CL):  13.844
Half-life (T1/2):  0.097

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.716
Drug-inuced Liver Injury (DILI):  0.889
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.888
Maximum Recommended Daily Dose:  0.21
Skin Sensitization:  0.921
Carcinogencity:  0.215
Eye Corrosion:  0.003
Eye Irritation:  0.703
Respiratory Toxicity:  0.9

Download Data

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

  Natural Product: NPC49041

Natural Product ID:  NPC49041
Common Name*:   BMEJCGKQLXCIJC-KRWDZBQOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BMEJCGKQLXCIJC-KRWDZBQOSA-N
Standard InCHI:  InChI=1S/C21H22O4/c1-12(2)9-10-15-19(23)13(3)21-18(20(15)24)16(22)11-17(25-21)14-7-5-4-6-8-14/h4-9,17,23-24H,10-11H2,1-3H3/t17-/m0/s1
SMILES:  CC(=CCc1c(c(C)c2c(C(=O)C[C@@H](c3ccccc3)O2)c1O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   179806
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0003646] 6-prenylated flavans
            • [CHEMONTID:0003507] 6-prenylated flavanones

*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
NPO28717 Miconia myriantha Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[11678651]
NPO27636 Hippasteria phrygiana Species Goniasteridae Eukaryota n.a. pacific n.a. PMID[16252922]
NPO27230 Eysenhardtia platycarpa Species Fabaceae Eukaryota n.a. branch n.a. PMID[17190443]
NPO27230 Eysenhardtia platycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[17190443]
NPO27449 Halichondria okadai Species Halichondriidae Eukaryota n.a. n.a. n.a. PMID[21410164]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28899 Eupatorium hyssopifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29365 Baileya multiradiata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29049 Sinoadina racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29049 Sinoadina racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29365 Baileya multiradiata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28899 Eupatorium hyssopifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29365 Baileya multiradiata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28884 Cladonia cryptochlorophaea Species Cladoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29049 Sinoadina racemosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27794 Acritopappus longifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27411 Liparis nakaharai Species Liparidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29365 Baileya multiradiata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27340 Campylopus clavatus Species Leucobryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9137 Tasmannia lanceolata Species Winteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28806 Populus grandidentata Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27449 Halichondria okadai Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28717 Miconia myriantha Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29345 Maytenus horrida Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28899 Eupatorium hyssopifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27709 Rhododendron maximum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29204 Picea breweriana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29467 Virola elongata Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27636 Hippasteria phrygiana Species Goniasteridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27173 Ramalina pollinaria Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27211 Adenocarpus hispanicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27131 Methylosinus trichosporium Species Methylocystaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29258 Virola oleifera Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29259 Streptomyces toyocaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27651 Cissus tricuspidata Species Vitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27756 Lepidiota negatoria Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6740 Amycolatopsis sulphurea Species Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO27194 Conger myriaster Species Congridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27837 Sarracenia flava Species Sarraceniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27594 Viola odorata Species Violaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27230 Eysenhardtia platycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29444 Erigeron linifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27074 Dermocybe semisanguinea Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27663 Onoseris lopezii Species Asteraceae 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

☑ 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 NPC49041 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 NPC49041 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