Structure

Physi-Chem Properties

Molecular Weight:  155.13
Volume:  176.477
LogP:  2.755
LogD:  2.957
LogS:  -2.814
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.388
Synthetic Accessibility Score:  3.193
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.484
MDCK Permeability:  2.2095076928962953e-05
Pgp-inhibitor:  0.02
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.316
30% Bioavailability (F30%):  0.019

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.84
Plasma Protein Binding (PPB):  81.41156768798828%
Volume Distribution (VD):  0.799
Pgp-substrate:  26.734838485717773%

ADMET: Metabolism

CYP1A2-inhibitor:  0.708
CYP1A2-substrate:  0.905
CYP2C19-inhibitor:  0.482
CYP2C19-substrate:  0.872
CYP2C9-inhibitor:  0.123
CYP2C9-substrate:  0.576
CYP2D6-inhibitor:  0.153
CYP2D6-substrate:  0.467
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.35

ADMET: Excretion

Clearance (CL):  11.213
Half-life (T1/2):  0.733

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.135
Drug-inuced Liver Injury (DILI):  0.252
AMES Toxicity:  0.044
Rat Oral Acute Toxicity:  0.891
Maximum Recommended Daily Dose:  0.377
Skin Sensitization:  0.84
Carcinogencity:  0.841
Eye Corrosion:  0.766
Eye Irritation:  0.956
Respiratory Toxicity:  0.953

Download Data

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

  Natural Product: NPC25407

Natural Product ID:  NPC25407
Common Name*:   NZGWDASTMWDZIW-VMIGTVKRSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NZGWDASTMWDZIW-VMIGTVKRSA-N
Standard InCHI:  InChI=1S/C10H16O/c1-7(2)9-5-4-8(3)6-10(9)11/h8H,4-6H2,1-3H3/i1+1,2+1,3+1
SMILES:  [13CH3]C(=C1CCC([13CH3])CC1=O)[13CH3]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11665448
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane monoterpenoids

*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
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[10514313]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. root n.a. PMID[10514313]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[11575962]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[15387651]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota flowers n.a. n.a. PMID[17190444]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota roots and rhizomes Shaoguan, Guangdong Province, China 2007-Dec PMID[20540535]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23327299]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. leaf n.a. PMID[24354205]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. twig n.a. PMID[24354205]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota leaves and stems n.a. n.a. PMID[25442304]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO27689 Mentha pulegium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30555 Mentha rotundifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23814 Elsholtzia splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29812 Panax quinquefolium Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8789 Schizonepeta tenuifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9247.1 Bupleurum smithii var. parvifolium Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10316 Glechoma longituba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28696 Rhaponticum uniflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31541 Caulis perillae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11329 Echinops grijsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5293 Caulis perillae frutescentis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO23814 Elsholtzia splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9247.1 Bupleurum smithii var. parvifolium Varieties Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15634 Radix smilacis Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28696 Rhaponticum uniflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27689 Mentha pulegium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11329 Echinops grijsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8789 Schizonepeta tenuifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10316 Glechoma longituba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11329 Echinops grijsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29812 Panax quinquefolium Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30555 Mentha rotundifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28696 Rhaponticum uniflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10316 Glechoma longituba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8789 Schizonepeta tenuifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11329 Echinops grijsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8789 Schizonepeta tenuifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28696 Rhaponticum uniflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10316 Glechoma longituba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6583 Clematis chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8789 Schizonepeta tenuifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2715 Murraya paniculata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20712 Panax quinquefolius Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10316 Glechoma longituba Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28696 Rhaponticum uniflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23814 Elsholtzia splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11329 Echinops grijsii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28919 Calendula officinalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27689 Mentha pulegium Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6583 Clematis chinensis 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 NPC25407 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 NPC25407 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