Structure

Physi-Chem Properties

Molecular Weight:  218.17
Volume:  245.844
LogP:  4.079
LogD:  3.812
LogS:  -3.858
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.568
Synthetic Accessibility Score:  4.505
Fsp3:  0.8
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:  -4.588
MDCK Permeability:  2.410834167676512e-05
Pgp-inhibitor:  0.18
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.898
30% Bioavailability (F30%):  0.326

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.949
Plasma Protein Binding (PPB):  63.616539001464844%
Volume Distribution (VD):  1.15
Pgp-substrate:  32.69519805908203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.117
CYP1A2-substrate:  0.283
CYP2C19-inhibitor:  0.237
CYP2C19-substrate:  0.859
CYP2C9-inhibitor:  0.238
CYP2C9-substrate:  0.541
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.323
CYP3A4-inhibitor:  0.335
CYP3A4-substrate:  0.331

ADMET: Excretion

Clearance (CL):  16.235
Half-life (T1/2):  0.155

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.113
Drug-inuced Liver Injury (DILI):  0.112
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.815
Maximum Recommended Daily Dose:  0.311
Skin Sensitization:  0.398
Carcinogencity:  0.26
Eye Corrosion:  0.969
Eye Irritation:  0.783
Respiratory Toxicity:  0.981

Download Data

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

  Natural Product: NPC87384

Natural Product ID:  NPC87384
Common Name*:   UGVIZCBJCSXBCJ-GCVYGYKWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UGVIZCBJCSXBCJ-GCVYGYKWSA-N
Standard InCHI:  InChI=1S/C15H22O/c1-9-6-5-7-10-8-11(16)12-13(14(12,2)3)15(9,10)4/h8-9,12-13H,5-7H2,1-4H3/t9-,12-,13+,15+/m0/s1
SMILES:  C[C@H]1CCCC2=CC(=O)[C@H]3[C@H](C3(C)C)[C@]12C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   12305213
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0003565] Aristolane 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
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. DOI[10.1016/0045-6535(91)90110-Y]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4039(01)90945-1]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. Isla Isabel (Gulf of California, Mexico) n.a. PMID[19007287]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[20476749]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[21563811]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. root n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. exocarp n.a. PMID[21800857]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota Rhizomes n.a. n.a. PMID[21936523]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[21936523]
NPO25682 Acorus calamus Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[22671987]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[22951040]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[23373216]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[23713285]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. PMID[24704449]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[26296476]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[26305406]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. PMID[26967731]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota Rhizomes n.a. n.a. PMID[29116780]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO163 Daucus carota Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5681 Acorus gramineus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20065 Astragalus lentiginosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16984 Pelargonium capitatum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8666 Acorus tatarinowii Species Acoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22796 Cyperus rotundus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12434 Salvia aspera Species Lamiaceae 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 NPC87384 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 NPC87384 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