Structure

Physi-Chem Properties

Molecular Weight:  262.05
Volume:  236.301
LogP:  -0.662
LogD:  -0.221
LogS:  -2.149
# Rotatable Bonds:  4
TPSA:  104.06
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.682
Synthetic Accessibility Score:  2.744
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.292
MDCK Permeability:  6.852691967651481e-06
Pgp-inhibitor:  0.004
Pgp-substrate:  0.867
Human Intestinal Absorption (HIA):  0.025
20% Bioavailability (F20%):  0.133
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  30.588237762451172%
Volume Distribution (VD):  0.643
Pgp-substrate:  66.86035919189453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.688
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.092
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.173
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.168
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.386

ADMET: Excretion

Clearance (CL):  2.667
Half-life (T1/2):  0.95

ADMET: Toxicity

hERG Blockers:  0.059
Human Hepatotoxicity (H-HT):  0.151
Drug-inuced Liver Injury (DILI):  0.635
AMES Toxicity:  0.108
Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.024
Skin Sensitization:  0.917
Carcinogencity:  0.03
Eye Corrosion:  0.003
Eye Irritation:  0.449
Respiratory Toxicity:  0.045

Download Data

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

  Natural Product: NPC176383

Natural Product ID:  NPC176383
Common Name*:   BNLKKFPQJANWMM-CYBMUJFWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BNLKKFPQJANWMM-CYBMUJFWSA-N
Standard InCHI:  InChI=1S/C15H18O5/c1-15(2,18)13(16)7-10-6-9-4-5-14(17)20-12(9)8-11(10)19-3/h4-6,8,13,16,18H,7H2,1-3H3/t13-/m1/s1
SMILES:  CC(C)([C@@H](Cc1cc2ccc(=O)oc2cc1OC)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   176475
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives

*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
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. DOI[10.5012/bkcs.2003.24.11.1699]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[12510838]
NPO16675 Peucedanum japonicum Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[1453177]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[15646793]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. leaf n.a. PMID[16926516]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[17238120]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18405608]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[18661821]
NPO27786 Eucalyptus dives Species Myrtaceae Eukaryota essential oils n.a. n.a. PMID[19191669]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21417376]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21627108]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[21657081]
NPO23380 Camellia japonica Species Theaceae Eukaryota flower buds n.a. n.a. PMID[22834923]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27444348]
NPO23380 Camellia japonica Species Theaceae Eukaryota Roots n.a. n.a. PMID[30395460]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota Roots n.a. n.a. PMID[31464439]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[32569471]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. root n.a. PMID[7700984]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18285 Daphne gnidium Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27786 Eucalyptus dives Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27786 Eucalyptus dives Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18285 Daphne gnidium Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16675 Peucedanum japonicum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16675 Peucedanum japonicum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16675 Peucedanum japonicum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19630 Taraxacum laevigatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22869 Penstemon grandiflorus Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22273 Angelica pubescens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18285 Daphne gnidium Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27786 Eucalyptus dives Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23274 Talaromyces tardifaciens Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23380 Camellia japonica Species Theaceae 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 NPC176383 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 NPC176383 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