Structure

Physi-Chem Properties

Molecular Weight:  452.5
Volume:  553.522
LogP:  13.055
LogD:  4.704
LogS:  -7.667
# Rotatable Bonds:  29
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.112
Synthetic Accessibility Score:  1.512
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.445
MDCK Permeability:  1.891412807708548e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.024
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.002
Plasma Protein Binding (PPB):  100.04943084716797%
Volume Distribution (VD):  4.94
Pgp-substrate:  0.7580012083053589%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.119
CYP2C19-inhibitor:  0.093
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.013
CYP2C9-substrate:  0.977
CYP2D6-inhibitor:  0.048
CYP2D6-substrate:  0.009
CYP3A4-inhibitor:  0.114
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  4.762
Half-life (T1/2):  0.009

ADMET: Toxicity

hERG Blockers:  0.647
Human Hepatotoxicity (H-HT):  0.004
Drug-inuced Liver Injury (DILI):  0.261
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.983
Carcinogencity:  0.014
Eye Corrosion:  0.996
Eye Irritation:  0.914
Respiratory Toxicity:  0.251

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

  Natural Product: NPC55800

Natural Product ID:  NPC55800
Common Name*:   DNLGLROXRPVTKW-JBOOMPGWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DNLGLROXRPVTKW-JBOOMPGWSA-N
Standard InCHI:  InChI=1S/C19H24O3/c1-4-5-6-7-15-14-10-11-19(3)17(22-19)9-8-13(2)16(14)12-21-18(15)20/h5,7,14,16-17H,1-2,6,8-12H2,3H3/b15-7-/t14-,16+,17+,19+/m1/s1
SMILES:  C=C=CC/C=C1/[C@H]2CC[C@@]3(C)[C@H](CCC(=C)[C@@H]2COC1=O)O3
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:0001244] Delta valerolactones

*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
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO23829 Salvia kronenburgii Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[14738403]
NPO21422 Ganoderma fornicatum Species Ganodermataceae Eukaryota fruiting bodies n.a. n.a. PMID[16989537]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[19778086]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Seed Essent. Oil n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Leaf Wax n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Pt n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26469 Thalictrum delavayi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21422 Ganoderma fornicatum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26721 Apium graveolens Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23829 Salvia kronenburgii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26469 Thalictrum delavayi Species Ranunculaceae 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 NPC55800 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 NPC55800 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