Structure

Physi-Chem Properties

Molecular Weight:  291.22
Volume:  311.599
LogP:  3.913
LogD:  3.834
LogS:  -3.708
# Rotatable Bonds:  2
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.695
Synthetic Accessibility Score:  5.525
Fsp3:  0.944
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:  -4.711
MDCK Permeability:  3.228960849810392e-05
Pgp-inhibitor:  0.092
Pgp-substrate:  0.911
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.653
30% Bioavailability (F30%):  0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.56
Plasma Protein Binding (PPB):  28.091524124145508%
Volume Distribution (VD):  0.997
Pgp-substrate:  50.81354522705078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.046
CYP1A2-substrate:  0.091
CYP2C19-inhibitor:  0.096
CYP2C19-substrate:  0.86
CYP2C9-inhibitor:  0.09
CYP2C9-substrate:  0.173
CYP2D6-inhibitor:  0.584
CYP2D6-substrate:  0.338
CYP3A4-inhibitor:  0.632
CYP3A4-substrate:  0.655

ADMET: Excretion

Clearance (CL):  5.2
Half-life (T1/2):  0.499

ADMET: Toxicity

hERG Blockers:  0.836
Human Hepatotoxicity (H-HT):  0.29
Drug-inuced Liver Injury (DILI):  0.91
AMES Toxicity:  0.295
Rat Oral Acute Toxicity:  0.535
Maximum Recommended Daily Dose:  0.182
Skin Sensitization:  0.965
Carcinogencity:  0.472
Eye Corrosion:  0.955
Eye Irritation:  0.746
Respiratory Toxicity:  0.966

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

  Natural Product: NPC303268

Natural Product ID:  NPC303268
Common Name*:   SZELUKCBWALJTL-JGPLCVHZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SZELUKCBWALJTL-JGPLCVHZSA-N
Standard InCHI:  InChI=1S/C18H29NO2/c1-12-9-14-10-17(21-13(2)20)16-6-4-8-19-7-3-5-15(14)18(16,19)11-12/h12,14-17H,3-11H2,1-2H3/t12-,14+,15-,16-,17+,18-/m1/s1
SMILES:  C[C@@H]1C[C@H]2C[C@@H]([C@H]3CCCN4CCC[C@H]2[C@]34C1)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. seed n.a. DOI[10.1016/S0031-9422(98)00552-4]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12932142]
NPO24855 Callicarpa americana Species Lamiaceae Eukaryota fruiting branches n.a. n.a. PMID[17279798]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29277 Lycopodium obscurum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21044 Sphaerellopsis filum Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26989 Delphinium geyeri Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24978 Psila boliviensis Species Psilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26662 Chrysanthemum foeniculaceum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29522 Cuscuta salina Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29428 Dalbergia cochinchinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24542 Doris obsoleta Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26775 Shorea wangtianshuea Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29460 Petiveria alliacea Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29277 Lycopodium obscurum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28418 Grateloupia filicina Species Halymeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27912 Cocculus laurifolius Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29521 Genista purgans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29247 Wahlenbergia marginata Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27937 Centaurea iberica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18357 Euphorbia sanctae-catharinae Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27125 Hovea linearis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24855 Callicarpa americana Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24832 Eriocaulon ligulatum Species Eriocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26339 Dillenia philippinensis Species Dilleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24225 Alexandrium peruvianum Species Gonyaulacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25798 Gunnera perpensa Species Gunneraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26498 Vernonia cumingiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22646 Malouetia tamaquarina Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28055 Perymenium berlandieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29087 Ligularia brachyphylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27361 Hylobius abietis Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29261 Bryothamnion triquetrum n.a. n.a. n.a. 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 NPC303268 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 NPC303268 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