Structure

Physi-Chem Properties

Molecular Weight:  104.05
Volume:  101.475
LogP:  -0.482
LogD:  -0.356
LogS:  0.709
# Rotatable Bonds:  2
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.458
Synthetic Accessibility Score:  2.729
Fsp3:  0.75
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:  -4.54
MDCK Permeability:  0.0008919088868424296
Pgp-inhibitor:  0.0
Pgp-substrate:  0.021
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.735

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.581
Plasma Protein Binding (PPB):  11.074321746826172%
Volume Distribution (VD):  0.804
Pgp-substrate:  86.14600372314453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.088
CYP1A2-substrate:  0.478
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.702
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.283
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.295
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.171

ADMET: Excretion

Clearance (CL):  5.29
Half-life (T1/2):  0.837

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.058
Drug-inuced Liver Injury (DILI):  0.087
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.178
Carcinogencity:  0.01
Eye Corrosion:  0.632
Eye Irritation:  0.983
Respiratory Toxicity:  0.073

Download Data

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

  Natural Product: NPC182215

Natural Product ID:  NPC182215
Common Name*:   LPEKGGXMPWTOCB-VKHMYHEASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LPEKGGXMPWTOCB-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C4H8O3/c1-3(5)4(6)7-2/h3,5H,1-2H3/t3-/m0/s1
SMILES:  C[C@@H](C(=O)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   94386
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001238] Carboxylic acid esters
            • [CHEMONTID:0003416] Methyl esters

*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
NPO1394 Penicillium sclerotigenum Species Aspergillaceae Eukaryota sclerotia n.a. n.a. PMID[10217735]
NPO25660 Gypsophila oldhamiana Species Caryophyllaceae Eukaryota n.a. root n.a. PMID[16880670]
NPO25660 Gypsophila oldhamiana Species Caryophyllaceae Eukaryota n.a. root n.a. PMID[17409564]
NPO25660 Gypsophila oldhamiana Species Caryophyllaceae Eukaryota roots n.a. n.a. PMID[18194870]
NPO28542 Streptocarpus dunnii Species Gesneriaceae Eukaryota n.a. n.a. n.a. PMID[21174407]
NPO28542 Streptocarpus dunnii Species Gesneriaceae Eukaryota n.a. n.a. n.a. PMID[22472691]
NPO13981 Helianthella quinquenervis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[8882437]
NPO9266 Stephania delavayi Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9266 Stephania delavayi Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11327 Lactarius necator Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29399 Microdochium nivale Species Microdochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25214 Uvaria narum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9266 Stephania delavayi Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25660 Gypsophila oldhamiana Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25660 Gypsophila oldhamiana Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28077 Phytophthora cactorum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7167 Hosta undulata Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13724 Garcinia celebica Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2040 Inocybe patouillardii Species Inocybaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23479 Elaeodendron buchananii Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25247 Dendrobium tosaense Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23613 Hypselodoris capensis Species Chromodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9266 Stephania delavayi Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25214 Uvaria narum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23374 Cortinarius bulbiger Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3471 Suillellus luridus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20655 Virola pavonis Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10785 Hypotrachyna neodamaziana Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11327 Lactarius necator Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29399 Microdochium nivale Species Microdochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25554 Yucca filifera Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1394 Penicillium sclerotigenum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25581 Coelospermum paniculatum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8243 Euphorbia supina Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10139 Sarcomelicope follicularis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28891 Trichocline reptans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13981 Helianthella quinquenervis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24350 Hammarbya paludosa Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28542 Streptocarpus dunnii Species Gesneriaceae 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 NPC182215 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 NPC182215 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