Structure

Physi-Chem Properties

Molecular Weight:  244.17
Volume:  257.372
LogP:  0.638
LogD:  0.869
LogS:  -1.767
# Rotatable Bonds:  2
TPSA:  80.92
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.536
Synthetic Accessibility Score:  4.545
Fsp3:  0.846
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.042
MDCK Permeability:  5.790337672806345e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.183
20% Bioavailability (F20%):  0.924
30% Bioavailability (F30%):  0.626

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.762
Plasma Protein Binding (PPB):  68.788330078125%
Volume Distribution (VD):  1.202
Pgp-substrate:  45.28519058227539%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.468
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.835
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.19
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.083
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.394

ADMET: Excretion

Clearance (CL):  4.301
Half-life (T1/2):  0.692

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.193
Drug-inuced Liver Injury (DILI):  0.021
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.121
Maximum Recommended Daily Dose:  0.958
Skin Sensitization:  0.115
Carcinogencity:  0.339
Eye Corrosion:  0.004
Eye Irritation:  0.217
Respiratory Toxicity:  0.531

Download Data

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

  Natural Product: NPC26020

Natural Product ID:  NPC26020
Common Name*:   CTCKPFXFWVNGLG-DWFSUXBBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CTCKPFXFWVNGLG-DWFSUXBBSA-N
Standard InCHI:  InChI=1S/C13H24O4/c1-9(14)5-6-13(17)11(2,3)7-10(15)8-12(13,4)16/h5-6,9-10,14-17H,7-8H2,1-4H3/b6-5+/t9-,10-,12+,13+/m0/s1
SMILES:  C[C@@H](/C=C/[C@]1(C(C)(C)C[C@@H](C[C@@]1(C)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   637237
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
NPO9771 Aka coralliphagum Species Niphatidae Eukaryota n.a. San Salvador in the Bahamas (12-26 m depth) 2001-MAR; 2003-JUL PMID[17309298]
NPO21139 Daphniphyllum calycinum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[19099464]
NPO19475 Isodon sculponeatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19697926]
NPO18418 Ficus microcarpa Species Moraceae Eukaryota leaves n.a. n.a. PMID[21194938]
NPO11402 Tithonia rotundifolia Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO8991 Carcinus maenas Species Carcinidae Eukaryota n.a. n.a. n.a. PMID[2421673]
NPO19475 Isodon sculponeatus Species Lamiaceae Eukaryota aerial parts Muli County, Sichuan Province, China 2011-AUG PMID[24219809]
NPO21139 Daphniphyllum calycinum Species Daphniphyllaceae Eukaryota n.a. leaf n.a. PMID[9599286]
NPO21482 Crotalaria laburnifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21482 Crotalaria laburnifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18418 Ficus microcarpa Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21139 Daphniphyllum calycinum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17508 Danae racemosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2627 Verbascum densiflorum Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5831 Mussaenda arcuata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24390 Juniperus rigida Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11758 Parmelia pokornyi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19768 Xylosalsola arbuscula Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19475 Isodon sculponeatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21482 Crotalaria laburnifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20336 Arctotheca calendula Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21139 Daphniphyllum calycinum Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17240 Crematogaster brevis Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14637 Saussurea cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9771 Aka coralliphagum Species Niphatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13119 Hymenoxys microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8991 Carcinus maenas Species Carcinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20115 Melampodium argophyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11402 Tithonia rotundifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19889 Cereus stellatus Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20470 Elaeagnus orientalis Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4385 Aconitum zuccarini Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16409 Quercus pedunculata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1506 Oldenlandia umbellata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1558 Ozothamnus obcordatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14222 Schefflera divaricata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16021 Boletus bovinus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6272 Chamaecyparis pisifera Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2684 Cortinarius vinosipes Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19763 Meloidogyne incognita Species Meloidogynidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20543 Psydrax livida Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21614 Urceolaria scruposa Species Trichodinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11166 Sclerodoris tanya n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14310 Tecoma heptaphylla Species Bignoniaceae 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 NPC26020 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 NPC26020 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