Structure

Physi-Chem Properties

Molecular Weight:  224.14
Volume:  231.469
LogP:  1.554
LogD:  2.286
LogS:  -3.476
# Rotatable Bonds:  1
TPSA:  49.83
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.687
Synthetic Accessibility Score:  4.967
Fsp3:  0.923
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:  -4.863
MDCK Permeability:  1.236417028849246e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.994
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.77
Plasma Protein Binding (PPB):  37.74468994140625%
Volume Distribution (VD):  1.214
Pgp-substrate:  52.84627151489258%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.975
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.894
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.088
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.397
CYP3A4-inhibitor:  0.038
CYP3A4-substrate:  0.562

ADMET: Excretion

Clearance (CL):  11.357
Half-life (T1/2):  0.758

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.302
Drug-inuced Liver Injury (DILI):  0.187
AMES Toxicity:  0.84
Rat Oral Acute Toxicity:  0.806
Maximum Recommended Daily Dose:  0.064
Skin Sensitization:  0.604
Carcinogencity:  0.07
Eye Corrosion:  0.97
Eye Irritation:  0.971
Respiratory Toxicity:  0.965

Download Data

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

  Natural Product: NPC30013

Natural Product ID:  NPC30013
Common Name*:   IDTQMVOQRHWPMV-KUUXYREKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  IDTQMVOQRHWPMV-KUUXYREKSA-N
Standard InCHI:  InChI=1S/C13H20O3/c1-7-10(15)5-4-9-6-13(8(2)14)11(16-13)12(7,9)3/h7,9-11,15H,4-6H2,1-3H3/t7-,9+,10-,11+,12+,13+/m0/s1
SMILES:  C[C@H]1[C@H](CC[C@@H]2C[C@@]3(C(=O)C)[C@@H]([C@]12C)O3)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15275909
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002012] Oxanes

*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
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. PMID[12662092]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. PMID[15679308]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. Caribbean n.a. PMID[1686898]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. stem n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[21226514]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. PMID[21226514]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[26281591]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[3404159]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota Pt n.a. n.a. Database[FooDB]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25140 Sapium sebiferum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5339 Isophysis tasmanica Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1203 Solanum pseudoquina Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10980 Petasites japonicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8433 Bongardia chrysogonum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17179 Elizabethkingia meningoseptica Species Flavobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO117 Acacia armata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1541 Clusia ellipticifolia Species Clusiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8132 Fritillaria meleagris Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5166 Adonis sutchuenensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2008 Streptomyces ehimensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13682 Lonchocarpus laxiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1396 Cladogynos orientalis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1706 Eragrostis curvula Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4836 Sideritis arborescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8950 Stilpnopappus pickelii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO643 Astragalus ernestii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21493 Bunodosoma caissarum Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8306 Berneuxia thibetica Species Diapensiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1049 Tethya amamensis Species Tethyidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6741 Metasequoia glyptostroboides Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7793 Matricaria matricarioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3445 Dumoria heckeli n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19991 Mantella aurantiaca Species Mantellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2323 Plantago lundborgii Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15275 Briareum asbestinum Species Briareidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25140 Sapium sebiferum Species Euphorbiaceae 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 NPC30013 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 NPC30013 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