Structure

Physi-Chem Properties

Molecular Weight:  284.07
Volume:  282.482
LogP:  3.238
LogD:  2.78
LogS:  -3.759
# Rotatable Bonds:  2
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.756
Synthetic Accessibility Score:  2.132
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:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.751
MDCK Permeability:  1.3659989235748071e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.986
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.828
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  96.7900619506836%
Volume Distribution (VD):  0.515
Pgp-substrate:  5.672348976135254%

ADMET: Metabolism

CYP1A2-inhibitor:  0.971
CYP1A2-substrate:  0.898
CYP2C19-inhibitor:  0.777
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.489
CYP2C9-substrate:  0.932
CYP2D6-inhibitor:  0.712
CYP2D6-substrate:  0.925
CYP3A4-inhibitor:  0.865
CYP3A4-substrate:  0.26

ADMET: Excretion

Clearance (CL):  6.867
Half-life (T1/2):  0.791

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.094
Drug-inuced Liver Injury (DILI):  0.894
AMES Toxicity:  0.17
Rat Oral Acute Toxicity:  0.086
Maximum Recommended Daily Dose:  0.748
Skin Sensitization:  0.879
Carcinogencity:  0.387
Eye Corrosion:  0.005
Eye Irritation:  0.935
Respiratory Toxicity:  0.324

Download Data

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

  Natural Product: NPC115323

Natural Product ID:  NPC115323
Common Name*:   OUMMPAFEQHTYIZ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OUMMPAFEQHTYIZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H12O5/c1-20-16-6-9(2-5-12(16)18)14-8-13(19)11-4-3-10(17)7-15(11)21-14/h2-8,17-18H,1H3
SMILES:  COc1cc(ccc1O)c1cc(=O)c2ccc(cc2o1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5281618
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002595] 3'-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
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4020(01)83306-8]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[10705751]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. stem n.a. PMID[11908963]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[12662094]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. seed n.a. PMID[12822897]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[15104480]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. bark n.a. PMID[15283458]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. leaf n.a. PMID[15340243]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. stem n.a. PMID[15577257]
NPO23510 Vicia faba Species Fabaceae Eukaryota flowers n.a. n.a. PMID[16180811]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota roots n.a. n.a. PMID[16989524]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[18064621]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. root n.a. PMID[18064621]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. branch n.a. PMID[22014228]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22014228]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22014228]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. rhizome n.a. PMID[22863942]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota aerial parts n.a. n.a. PMID[24042007]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. root n.a. PMID[24257774]
NPO40372 Tephrosia linearis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[32155073]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9051910]
NPO23510 Vicia faba Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO23510 Vicia faba Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26473 Garcinia eugeniifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23510 Vicia faba Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26473 Garcinia eugeniifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27260 Polygala tenuifolia Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO403 Gentiana lutea Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19488 Trifolium subterraneum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12181 Albizia julibrissin Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25528 Calophyllum brasiliense Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23510 Vicia faba Species Fabaceae 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
NPO23510 NPC115323 Other (raw) Fruit 0.301 0.002 0.6 mg/100g Database [DUKE]
NPO23510 NPC115323 Raw n.a. 0.070000002 n.a. n.a. mg/100g Database [PHENOL EXPLORER]

☑ 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
NPT927 Cell Line PBMC Homo sapiens Activity = 109.22 % PMID[32155073]
NPT927 Cell Line PBMC Homo sapiens Activity = 57.64 % PMID[32155073]
NPT927 Cell Line PBMC Homo sapiens Activity = 100.0 % PMID[32155073]
NPT927 Cell Line PBMC Homo sapiens Activity = 92.58 % PMID[32155073]
NPT927 Cell Line PBMC Homo sapiens Activity = 3.64 % PMID[32155073]

☑ 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 NPC115323 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 NPC115323 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