Structure

Physi-Chem Properties

Molecular Weight:  298.05
Volume:  288.636
LogP:  3.979
LogD:  1.796
LogS:  -4.024
# Rotatable Bonds:  1
TPSA:  111.9
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.632
Synthetic Accessibility Score:  2.356
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.178
MDCK Permeability:  7.968677891767584e-06
Pgp-inhibitor:  0.054
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.064
20% Bioavailability (F20%):  0.067
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.058
Plasma Protein Binding (PPB):  97.8523941040039%
Volume Distribution (VD):  0.53
Pgp-substrate:  1.4939101934432983%

ADMET: Metabolism

CYP1A2-inhibitor:  0.457
CYP1A2-substrate:  0.095
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.449
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.077
CYP2D6-substrate:  0.099
CYP3A4-inhibitor:  0.126
CYP3A4-substrate:  0.074

ADMET: Excretion

Clearance (CL):  0.932
Half-life (T1/2):  0.614

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.304
Drug-inuced Liver Injury (DILI):  0.988
AMES Toxicity:  0.829
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.127
Skin Sensitization:  0.459
Carcinogencity:  0.178
Eye Corrosion:  0.003
Eye Irritation:  0.632
Respiratory Toxicity:  0.109

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Similar NPs/Drugs  

  Natural Product: NPC243062

Natural Product ID:  NPC243062
Common Name*:   ZOUBDBLFNYDFPG-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZOUBDBLFNYDFPG-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H10O6/c1-6-2-8-12(10(17)3-6)15(20)13-9(14(8)19)4-7(16(21)22)5-11(13)18/h2-5,17-18H,1H3,(H,21,22)
SMILES:  Cc1cc2c(c(c1)O)C(=O)c1c(cc(cc1O)C(=O)O)C2=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3009664
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes
        • [CHEMONTID:0001911] Anthracenecarboxylic acids and derivatives
          • [CHEMONTID:0002424] Anthracenecarboxylic acids

*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
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.lwt.2014.11.023]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[11076555]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[11459643]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota leaves n.a. n.a. PMID[12568545]
NPO30021 Rheum emodi Species Polygonaceae Eukaryota Roots Gorkha district, Nepal 1996-OCT PMID[12932135]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[1517743]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. root n.a. PMID[16564530]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. seed n.a. PMID[17345316]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19191562]
NPO31520 Polygonum multiflorum Species Polygonaceae Eukaryota roots n.a. n.a. PMID[24499304]
NPO31136 Cassia tora Species Fabaceae Eukaryota seeds n.a. n.a. PMID[26483136]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota Whole Plants n.a. n.a. PMID[28093914]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[29359942]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[31944695]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota Roots; Tubers n.a. n.a. PMID[7714535]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[8277318]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12220 Hemerocallis thunbergii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30811 Cassia angustifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30021 Rheum emodi Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29776 Cassia acutifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31520 Polygonum multiflorum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31136 Cassia tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29780 Cassia mimosoides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12759 Rheum australe Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13 Chamaecrista mimosoides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9148 Caulis polygoni multiflori n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27034 Radix et rhizoma rhei praeparata Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4195 Radix et rhizoma rhei Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12220 Hemerocallis thunbergii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12834 Radix polygoni multiflori preparata Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7672 Senna tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31520 Polygonum multiflorum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29780 Cassia mimosoides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30811 Cassia angustifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29776 Cassia acutifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31136 Cassia tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29417 Fallopia multiflora Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7672 Senna tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7672 Senna tora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12220 Hemerocallis thunbergii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13 Chamaecrista mimosoides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12759 Rheum australe Species Polygonaceae 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 NPC243062 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 NPC243062 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