Structure

Physi-Chem Properties

Molecular Weight:  346.21
Volume:  376.638
LogP:  2.9
LogD:  2.045
LogS:  -3.918
# Rotatable Bonds:  2
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.582
Synthetic Accessibility Score:  5.798
Fsp3:  0.619
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:  -4.622
MDCK Permeability:  2.8147202101536095e-05
Pgp-inhibitor:  0.222
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.08
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.963
Plasma Protein Binding (PPB):  50.692195892333984%
Volume Distribution (VD):  1.096
Pgp-substrate:  58.27119827270508%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.127
CYP2C19-inhibitor:  0.212
CYP2C19-substrate:  0.86
CYP2C9-inhibitor:  0.091
CYP2C9-substrate:  0.262
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.482
CYP3A4-inhibitor:  0.409
CYP3A4-substrate:  0.471

ADMET: Excretion

Clearance (CL):  12.09
Half-life (T1/2):  0.244

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.629
Drug-inuced Liver Injury (DILI):  0.104
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.635
Maximum Recommended Daily Dose:  0.978
Skin Sensitization:  0.69
Carcinogencity:  0.886
Eye Corrosion:  0.003
Eye Irritation:  0.016
Respiratory Toxicity:  0.889

Download Data

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

  Natural Product: NPC280554

Natural Product ID:  NPC280554
Common Name*:   MEZXULZUADULAO-MEDRYPNSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MEZXULZUADULAO-MEDRYPNSSA-N
Standard InCHI:  InChI=1S/C21H30O4/c1-13-6-7-15-8-9-17(20(24)25-5)19(21(15,3)4)18(23)12-14(2)11-16(22)10-13/h11,15-16,22H,1,6-10,12H2,2-5H3/b14-11+/t15-,16+/m1/s1
SMILES:  C=C1CC[C@@H]2CCC(=C(C(=O)C/C(=C/[C@H](C1)O)/C)C2(C)C)C(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. PMID[12398538]
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. PMID[16933873]
NPO22004 Cystodytes solitus Species Polycitoridae Eukaryota n.a. n.a. n.a. PMID[18484775]
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. PMID[19061391]
NPO24805 Thorecta reticulata Species Thorectidae Eukaryota n.a. n.a. n.a. PMID[21513294]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25343 Tanacetum microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25343 Tanacetum microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25314 Usnea ceratina Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22004 Cystodytes solitus Species Polycitoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23999 Rhipidothuria racowitzai n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25655 Pseudocyphellaria granulata Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6639 Flagelloscypha pilatii Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2404 Heterophragma quadriloculare Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24482 Phyllanthus oxyphyllus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25427 Solanum vespertilio Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25516 Dahlia sherffii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25452 Crucigenia apiculata Species Scenedesmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25548 Balanophora indica Species Balanophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28702 Cyclolepis genistoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23333 Michelia excelsa Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25485 Agathosma lanceolata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20428 Debregeasia salicifolia Species Urticaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19210 Quercus lusitanica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25061 Lactarius glyciosmus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11177 0ctiluca scintillans Species 0ctilucaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5278 Acacia cyperophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24616 Ottonia vahlii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5543 Persicaria tomentosa Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25205 Thymus borgiae Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3706 Hedypnois rhagadioloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24310 Cespitularia hypotentaculata Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24805 Thorecta reticulata Species Thorectidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25343 Tanacetum microphyllum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24435 Beschorneria bracteata Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25684 Fagus dombeyi Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25606 Aster patagonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25631 Picris kamtschatica Species Asteraceae 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 NPC280554 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 NPC280554 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