Structure

Physi-Chem Properties

Molecular Weight:  239.13
Volume:  275.431
LogP:  3.145
LogD:  2.458
LogS:  -3.137
# Rotatable Bonds:  5
TPSA:  20.31
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.545
Synthetic Accessibility Score:  4.005
Fsp3:  0.312
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.158
MDCK Permeability:  5.084276926936582e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.214
20% Bioavailability (F20%):  0.02
30% Bioavailability (F30%):  0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.678
Plasma Protein Binding (PPB):  93.04569244384766%
Volume Distribution (VD):  0.777
Pgp-substrate:  2.2390575408935547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.528
CYP1A2-substrate:  0.42
CYP2C19-inhibitor:  0.95
CYP2C19-substrate:  0.481
CYP2C9-inhibitor:  0.893
CYP2C9-substrate:  0.923
CYP2D6-inhibitor:  0.55
CYP2D6-substrate:  0.855
CYP3A4-inhibitor:  0.881
CYP3A4-substrate:  0.347

ADMET: Excretion

Clearance (CL):  7.831
Half-life (T1/2):  0.575

ADMET: Toxicity

hERG Blockers:  0.059
Human Hepatotoxicity (H-HT):  0.924
Drug-inuced Liver Injury (DILI):  0.232
AMES Toxicity:  0.063
Rat Oral Acute Toxicity:  0.818
Maximum Recommended Daily Dose:  0.741
Skin Sensitization:  0.987
Carcinogencity:  0.898
Eye Corrosion:  0.468
Eye Irritation:  0.834
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC31206

Natural Product ID:  NPC31206
Common Name*:   OGBLCPGFTJJOTG-AWGJLQHSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OGBLCPGFTJJOTG-AWGJLQHSSA-N
Standard InCHI:  InChI=1S/C16H17NO/c1-2-3-4-5-6-7-8-10-13-16(18)17-14-11-9-12-15-17/h1,7-8,10-11,13-14H,5-6,9,12,15H2/b8-7+,13-10+
SMILES:  C#CC#CCC/C=C/C=C/C(=O)N1C=CCCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14427416
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines
          • [CHEMONTID:0001934] Tetrahydropyridines

*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
NPO14864 Clerodendrum cyrtophyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[11473423]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11575948]
NPO12347 Pseudomonas syringae Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[14714872]
NPO15548 Sinularia leptoclados Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[16724859]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7042 Myrica arborea Species Myricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8392 Iryanthera polyneura Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4699 Dracaena ombet Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12347 Pseudomonas syringae Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8392 Iryanthera polyneura Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11151 Arnebia decumbens Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19872 Achillea magnifica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10210 Artabotrys uncinatus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9734 Vincetoxicum hirundinaria Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4503 Bryonopsis laciniosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14864 Clerodendrum cyrtophyllum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20070 Crinum stuhlmannii Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11683 Crotalaria mitchellii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12539 Lissoclinum japonicum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5469 Pseudoxandra sclerocarpa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22084 Stypandra imbricata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7042 Myrica arborea Species Myricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4518.1 Saccharothrix mutabilis subsp. capreolus Subspecies Pseudonocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12993 Polypodium vulgare Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6367 Cortinarius viola Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15166 Cephalotaxus hainanensis Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13549 Otanthus maritimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26712 Cladrastis kentukea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12121 Streptomyces naraensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3974 Ferula gummosa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14989 Acanthothamnus aphyllus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13320 Glycosmis puberula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11505 Nigella aristata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9338 Polygala aureocauda Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14191 Berkheya rhapontica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15066 Iridaea membranacea Species Gigartinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15548 Sinularia leptoclados Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1027 Scrophularia leucoclada Species Scrophulariaceae 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 NPC31206 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 NPC31206 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