Structure

Physi-Chem Properties

Molecular Weight:  160.11
Volume:  170.659
LogP:  1.382
LogD:  1.108
LogS:  -1.132
# Rotatable Bonds:  6
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.484
Synthetic Accessibility Score:  2.485
Fsp3:  0.875
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:  -4.331
MDCK Permeability:  0.00010008941171690822
Pgp-inhibitor:  0.005
Pgp-substrate:  0.033
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.648

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.755
Plasma Protein Binding (PPB):  24.829744338989258%
Volume Distribution (VD):  0.715
Pgp-substrate:  70.83869934082031%

ADMET: Metabolism

CYP1A2-inhibitor:  0.497
CYP1A2-substrate:  0.213
CYP2C19-inhibitor:  0.178
CYP2C19-substrate:  0.657
CYP2C9-inhibitor:  0.058
CYP2C9-substrate:  0.298
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.132
CYP3A4-inhibitor:  0.016
CYP3A4-substrate:  0.212

ADMET: Excretion

Clearance (CL):  11.431
Half-life (T1/2):  0.855

ADMET: Toxicity

hERG Blockers:  0.05
Human Hepatotoxicity (H-HT):  0.024
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.023
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.104
Skin Sensitization:  0.345
Carcinogencity:  0.757
Eye Corrosion:  0.983
Eye Irritation:  0.987
Respiratory Toxicity:  0.077

Download Data

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

  Natural Product: NPC150210

Natural Product ID:  NPC150210
Common Name*:   LHDWRKCOQQHAMP-ZETCQYMHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LHDWRKCOQQHAMP-ZETCQYMHSA-N
Standard InCHI:  InChI=1S/C8H16O3/c1-3-4-5-11-8(10)6-7(2)9/h7,9H,3-6H2,1-2H3/t7-/m0/s1
SMILES:  CCCCOC(=O)C[C@H](C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11019159
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0001713] Beta hydroxy acids and derivatives

*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
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. n.a. n.a. PMID[15743176]
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. Hawaiian n.a. PMID[18407693]
NPO12963 Angelica anomala Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25933 Elysia rufescens Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26460 Serratia odorifera Species Yersiniaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26303 Tacca esquirolii Species Taccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25777 Acacia longifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26593 Astragalus canadensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12963 Angelica anomala Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26735 Stevia amambayensis 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 NPC150210 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 NPC150210 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