Structure

Physi-Chem Properties

Molecular Weight:  342.07
Volume:  332.018
LogP:  2.467
LogD:  2.054
LogS:  -3.801
# Rotatable Bonds:  4
TPSA:  117.2
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.622
Synthetic Accessibility Score:  3.104
Fsp3:  0.111
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.956
MDCK Permeability:  9.157093700196128e-06
Pgp-inhibitor:  0.003
Pgp-substrate:  0.982
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.072
30% Bioavailability (F30%):  0.212

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.015
Plasma Protein Binding (PPB):  97.17108154296875%
Volume Distribution (VD):  0.497
Pgp-substrate:  2.986690044403076%

ADMET: Metabolism

CYP1A2-inhibitor:  0.944
CYP1A2-substrate:  0.386
CYP2C19-inhibitor:  0.518
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.589
CYP2C9-substrate:  0.929
CYP2D6-inhibitor:  0.556
CYP2D6-substrate:  0.804
CYP3A4-inhibitor:  0.541
CYP3A4-substrate:  0.171

ADMET: Excretion

Clearance (CL):  5.368
Half-life (T1/2):  0.862

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.243
Drug-inuced Liver Injury (DILI):  0.936
AMES Toxicity:  0.333
Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.818
Skin Sensitization:  0.648
Carcinogencity:  0.278
Eye Corrosion:  0.005
Eye Irritation:  0.859
Respiratory Toxicity:  0.295

Download Data

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

  Natural Product: NPC103212

Natural Product ID:  NPC103212
Common Name*:   HATNSSGJRODWED-SECBINFHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HATNSSGJRODWED-SECBINFHSA-N
Standard InCHI:  InChI=1S/C18H14O7/c1-9(19)18(23)24-12-6-13(21)17-14(22)8-15(25-16(17)7-12)10-2-4-11(20)5-3-10/h2-9,19-21H,1H3/t9-/m1/s1
SMILES:  C[C@H](C(=O)Oc1cc(c2c(=O)cc(c3ccc(cc3)O)oc2c1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones

*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
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. twig n.a. PMID[14709876]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. leaf n.a. PMID[14709876]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota Leaves; Twigs n.a. n.a. PMID[15043402]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota stem wood n.a. n.a. PMID[16180806]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[16309320]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota leaves n.a. n.a. PMID[16792412]
NPO23769 Ainsliaea macrocephala Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[18484734]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[18489163]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19128011]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota leaves and stems Kunming, Yunnan, China 2007-AUG PMID[19133780]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21478 Buxus hyrcana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23428 Tinus mamillata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25080 Sphaeria maculans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23721 Epidendrum rigidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23896 Cytisus ratisbonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23769 Ainsliaea macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21478 Buxus hyrcana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20498 Cephalaria ambrosioides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23474 Abies veitchii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23849 Dicoma anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24015 Perknaster fuscus Species Ganeriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22684 Enrichment culture Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24258 Vellozia nivea Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21352 Boronia ternata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24462 Pityrogramma ebenea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28748 Aphis sambuci Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18918 Lecanicillium muscarium Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23930 Luculia pinceana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24993 Conospermum teretifolium Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24952 Galeopsis tetrahit Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7197 Colchicum robustum Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18735 Pinus mugo Species Pinaceae 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 NPC103212 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 NPC103212 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