Structure

Physi-Chem Properties

Molecular Weight:  300.17
Volume:  336.539
LogP:  5.09
LogD:  4.183
LogS:  -4.045
# Rotatable Bonds:  7
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.565
Synthetic Accessibility Score:  2.615
Fsp3:  0.316
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:  -4.974
MDCK Permeability:  2.123270860465709e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.061
Human Intestinal Absorption (HIA):  0.084
20% Bioavailability (F20%):  0.035
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.035
Plasma Protein Binding (PPB):  100.11276245117188%
Volume Distribution (VD):  0.15
Pgp-substrate:  0.7886073589324951%

ADMET: Metabolism

CYP1A2-inhibitor:  0.316
CYP1A2-substrate:  0.151
CYP2C19-inhibitor:  0.093
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.601
CYP2C9-substrate:  0.752
CYP2D6-inhibitor:  0.563
CYP2D6-substrate:  0.238
CYP3A4-inhibitor:  0.052
CYP3A4-substrate:  0.097

ADMET: Excretion

Clearance (CL):  3.814
Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.929
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.472
Skin Sensitization:  0.957
Carcinogencity:  0.078
Eye Corrosion:  0.014
Eye Irritation:  0.775
Respiratory Toxicity:  0.373

Download Data

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

  Natural Product: NPC230660

Natural Product ID:  NPC230660
Common Name*:   BGVUWLLRNRBDAY-GDBMZVCRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BGVUWLLRNRBDAY-GDBMZVCRSA-N
Standard InCHI:  InChI=1S/C16H18N2O/c1-16(19)7-12-11-4-3-5-13-15(11)10(8-17-13)6-14(12)18(2)9-16/h3-5,7-8,14,17,19H,6,9H2,1-2H3/t14-,16-/m1/s1
SMILES:  C[C@]1(C=C2c3cccc4c3c(C[C@H]2N(C)C1)c[nH]4)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11644551
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002679] Ergoline and derivatives
        • [CHEMONTID:0002747] Clavines 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
NPO15336 Prunus avium Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1016/j.foodchem.2007.08.004]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. fruit n.a. DOI[10.1016/j.phytochem.2007.01.008]
NPO3710 Erythrina zeyheri Species Fabaceae Eukaryota n.a. root n.a. PMID[15597305]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. fruit n.a. PMID[17328933]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[17841110]
NPO14341 Phakellia fusca Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[20345147]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20778930]
NPO6245 Festuca rubra Species Poaceae Eukaryota n.a. root n.a. PMID[22192329]
NPO3206 Karwinskia parvifolia Species Rhamnaceae Eukaryota Fruits n.a. n.a. PMID[25402632]
NPO14341 Phakellia fusca Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[30844272]
NPO18098 Topsentia ophiraphidites Species Eukaryota n.a. n.a. n.a. PMID[7714543]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15336 Prunus avium Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO12320 Adonis amurensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15336 Prunus avium Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3710 Erythrina zeyheri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12320 Adonis amurensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12320 Adonis amurensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12320 Adonis amurensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15530 Geum bulgaricum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3710 Erythrina zeyheri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15336 Prunus avium Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18098 Topsentia ophiraphidites Species Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6245 Festuca rubra Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24009 Claviceps purpurea Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3206 Karwinskia parvifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14341 Phakellia fusca Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7563 Soulamea fraxinifolia Species Simaroubaceae 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 NPC230660 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 NPC230660 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