Structure

Physi-Chem Properties

Molecular Weight:  258.09
Volume:  261.669
LogP:  2.059
LogD:  2.273
LogS:  -4.289
# Rotatable Bonds:  0
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.72
Synthetic Accessibility Score:  3.703
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.729
MDCK Permeability:  1.9159782823408023e-05
Pgp-inhibitor:  0.02
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.032

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.088
Plasma Protein Binding (PPB):  92.27349090576172%
Volume Distribution (VD):  0.942
Pgp-substrate:  4.551711559295654%

ADMET: Metabolism

CYP1A2-inhibitor:  0.986
CYP1A2-substrate:  0.763
CYP2C19-inhibitor:  0.731
CYP2C19-substrate:  0.224
CYP2C9-inhibitor:  0.383
CYP2C9-substrate:  0.554
CYP2D6-inhibitor:  0.923
CYP2D6-substrate:  0.125
CYP3A4-inhibitor:  0.837
CYP3A4-substrate:  0.229

ADMET: Excretion

Clearance (CL):  3.315
Half-life (T1/2):  0.125

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.062
Drug-inuced Liver Injury (DILI):  0.71
AMES Toxicity:  0.875
Rat Oral Acute Toxicity:  0.274
Maximum Recommended Daily Dose:  0.47
Skin Sensitization:  0.287
Carcinogencity:  0.704
Eye Corrosion:  0.004
Eye Irritation:  0.823
Respiratory Toxicity:  0.135

Download Data

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

  Natural Product: NPC84410

Natural Product ID:  NPC84410
Common Name*:   HUXMQAHWPMWHPJ-HNNXBMFYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HUXMQAHWPMWHPJ-HNNXBMFYSA-N
Standard InCHI:  InChI=1S/C15H14O4/c1-7-4-5-9-11-10(7)13(17)12(16)8(2)14(11)19-6-15(9,3)18/h4-5,18H,6H2,1-3H3/t15-/m0/s1
SMILES:  Cc1ccc2c3c1C(=O)C(=O)C(=C3OC[C@]2(C)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000023] Naphthalenes
        • [CHEMONTID:0000153] Naphthoquinones

*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
NPO6427 Wardomyces anomalus Species Microascaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np020518b]
NPO6427 Wardomyces anomalus Species Microascaceae Eukaryota n.a. n.a. n.a. PMID[12762814]
NPO19460 Karenia brevis Species Kareniaceae Eukaryota n.a. n.a. n.a. PMID[15679307]
NPO5167 Peripentadenia mearsii Species Elaeocarpaceae Eukaryota n.a. Australian rainforest n.a. PMID[18039010]
NPO19460 Karenia brevis Species Kareniaceae Eukaryota n.a. n.a. n.a. PMID[20218657]
NPO10455 Vaccinium uliginosum Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10455 Vaccinium uliginosum Species Ericaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO960 Phlomis aurea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10455 Vaccinium uliginosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2124 Bulgaria inquinans Species Bulgariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO960 Phlomis aurea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6423 Vitex cauliflora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17202 Lasallia asiae-orientalis Species Umbilicariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9794 Dysoxylum fraseranum Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3546 Shorea balangeran Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10273 Dictyota flabellata Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25866 Kaunia lasiophthalma Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8878 Polygala arenaria Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13058 Psychotria brachyceras Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11158 Diplopterygium rufopilosum Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19460 Karenia brevis Species Kareniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7535 Mansonia altissima Species Culicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6878 Vesperus xatarti Species Cerambycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11510 Astragalus flavescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11354 Streptomyces galbus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12123 Geodia gigas Species Geodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6427 Wardomyces anomalus Species Microascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4348 Watasenia scintillans Species Enoploteuthidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24924 Saara hardwickii Species Agamidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9565 Linum maritimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5167 Peripentadenia mearsii Species Elaeocarpaceae 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 NPC84410 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 NPC84410 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