Structure

Physi-Chem Properties

Molecular Weight:  264.14
Volume:  269.578
LogP:  1.643
LogD:  1.979
LogS:  -3.159
# Rotatable Bonds:  0
TPSA:  59.06
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.313
Synthetic Accessibility Score:  4.936
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.784
MDCK Permeability:  3.0148663427098654e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.826
20% Bioavailability (F20%):  0.494
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.847
Plasma Protein Binding (PPB):  77.95796966552734%
Volume Distribution (VD):  1.001
Pgp-substrate:  26.025306701660156%

ADMET: Metabolism

CYP1A2-inhibitor:  0.055
CYP1A2-substrate:  0.306
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.745
CYP2C9-inhibitor:  0.048
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.13
CYP3A4-inhibitor:  0.084
CYP3A4-substrate:  0.282

ADMET: Excretion

Clearance (CL):  11.837
Half-life (T1/2):  0.61

ADMET: Toxicity

hERG Blockers:  0.022
Human Hepatotoxicity (H-HT):  0.499
Drug-inuced Liver Injury (DILI):  0.316
AMES Toxicity:  0.202
Rat Oral Acute Toxicity:  0.859
Maximum Recommended Daily Dose:  0.539
Skin Sensitization:  0.811
Carcinogencity:  0.466
Eye Corrosion:  0.603
Eye Irritation:  0.705
Respiratory Toxicity:  0.978

Download Data

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

  Natural Product: NPC16505

Natural Product ID:  NPC16505
Common Name*:   WMVRNUCMFRNMFV-JGHPKWLMSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  WMVRNUCMFRNMFV-JGHPKWLMSA-N
Standard InCHI:  InChI=1S/C15H20O4/c1-8-4-5-12-15(3,19-12)7-11-13(10(16)6-8)9(2)14(17)18-11/h6,10-13,16H,2,4-5,7H2,1,3H3/b8-6+/t10-,11-,12+,13+,15-/m0/s1
SMILES:  C/C/1=C[C@@H]([C@H]2C(=C)C(=O)O[C@H]2C[C@@]2(C)[C@@H](CC1)O2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. Philippines n.a. PMID[12193033]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. n.a. n.a. PMID[12350152]
NPO15105 Lyngbya semiplena Species Oscillatoriaceae Bacteria n.a. Papua New Guinea n.a. PMID[14575438]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota Root Bark n.a. n.a. PMID[21985060]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota n.a. root n.a. PMID[21985060]
NPO19302 Amathia alternata Species Vesiculariidae Eukaryota n.a. Atlantic n.a. PMID[9249973]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18669 Myriophyllum verticillatum Species Haloragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13667 Manoao colensoi Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11070 Nervilia purpurea Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25840 Sargassum fusiforme Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12968 Crotalaria spectabilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19302 Amathia alternata Species Vesiculariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18035 Lagerstroemia flos-reginae Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19079 Vatica pauciflora Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22538 Dendrobium plicatile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15105 Lyngbya semiplena Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1762 Citropsis articulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16082 Flindersia bennettiana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13312 Senecio panduriformis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10039 Podosphaera fuliginea Species Erysiphaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14198 Haliclona valliculata Species Chalinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17744 Litsea elliptica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11960 Myriastra clavosa Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14705 Tanacetopsis mucronata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19237 Sargassum macrocarpum Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18258 Zanthoxylum rhoifolium Species Rutaceae 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 NPC16505 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 NPC16505 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