Structure

Physi-Chem Properties

Molecular Weight:  300.06
Volume:  291.273
LogP:  3.171
LogD:  2.239
LogS:  -3.765
# Rotatable Bonds:  2
TPSA:  100.13
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.629
Synthetic Accessibility Score:  2.326
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.99
MDCK Permeability:  1.2580145266838372e-05
Pgp-inhibitor:  0.183
Pgp-substrate:  0.079
Human Intestinal Absorption (HIA):  0.029
20% Bioavailability (F20%):  0.138
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.005
Plasma Protein Binding (PPB):  96.06243133544922%
Volume Distribution (VD):  0.59
Pgp-substrate:  9.14354133605957%

ADMET: Metabolism

CYP1A2-inhibitor:  0.954
CYP1A2-substrate:  0.737
CYP2C19-inhibitor:  0.161
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.617
CYP2C9-substrate:  0.714
CYP2D6-inhibitor:  0.519
CYP2D6-substrate:  0.496
CYP3A4-inhibitor:  0.261
CYP3A4-substrate:  0.149

ADMET: Excretion

Clearance (CL):  5.751
Half-life (T1/2):  0.838

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.174
Drug-inuced Liver Injury (DILI):  0.977
AMES Toxicity:  0.489
Rat Oral Acute Toxicity:  0.181
Maximum Recommended Daily Dose:  0.539
Skin Sensitization:  0.924
Carcinogencity:  0.317
Eye Corrosion:  0.003
Eye Irritation:  0.663
Respiratory Toxicity:  0.278

Download Data

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

  Natural Product: NPC144233

Natural Product ID:  NPC144233
Common Name*:   YXKBIVMXBJYKCD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YXKBIVMXBJYKCD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H12O6/c1-21-9-4-2-8(3-5-9)13-7-11(17)10-6-12(18)14(19)15(20)16(10)22-13/h2-7,18-20H,1H3
SMILES:  COc1ccc(cc1)c1cc(=O)c2cc(c(c(c2o1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   16657777
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002596] 4'-O-methylated flavonoids

*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
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[11678666]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12027772]
NPO23098 Aglaia silvestris Species Meliaceae Eukaryota n.a. fruit n.a. PMID[15132542]
NPO23098 Aglaia silvestris Species Meliaceae Eukaryota n.a. twig n.a. PMID[15132542]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15184162]
NPO23527 Croton laevigatus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[20307086]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. latex n.a. PMID[21854017]
NPO22238 Inula falconeri Species Asteraceae Eukaryota aerial parts Tibet, China n.a. PMID[21924800]
NPO22803 Neolitsea parvigemma Species Lauraceae Eukaryota n.a. leaf n.a. PMID[21941915]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22103394]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24738739]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO4608 Aesculus californica Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21872 Hemerocallis longituba Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21872 Hemerocallis longituba Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4608 Aesculus californica Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4608 Aesculus californica Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23098 Aglaia silvestris Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21501 Mycale tenuispiculata Species Mycalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17815 Verbesina occidentalis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24362 Polygonum plebejum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23915 Asplenium fontanum Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18855 Isolona ghesquierei Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23496 Agathosma spinosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4608 Aesculus californica Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20354 Genista cadasonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22695 Hemsleya chinensis Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22803 Neolitsea parvigemma Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21872 Hemerocallis longituba Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23527 Croton laevigatus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22238 Inula falconeri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20609 Mikania banisteriae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23278 Colubrina granulosa Species Rhamnaceae 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 NPC144233 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 NPC144233 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