Structure

Physi-Chem Properties

Molecular Weight:  343.11
Volume:  342.781
LogP:  1.09
LogD:  0.667
LogS:  -2.03
# Rotatable Bonds:  7
TPSA:  127.42
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.469
Synthetic Accessibility Score:  2.589
Fsp3:  0.167
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:  -5.742
MDCK Permeability:  9.373028660775162e-06
Pgp-inhibitor:  0.002
Pgp-substrate:  0.011
Human Intestinal Absorption (HIA):  0.86
20% Bioavailability (F20%):  0.983
30% Bioavailability (F30%):  0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.013
Plasma Protein Binding (PPB):  94.36302947998047%
Volume Distribution (VD):  0.311
Pgp-substrate:  4.8708624839782715%

ADMET: Metabolism

CYP1A2-inhibitor:  0.229
CYP1A2-substrate:  0.046
CYP2C19-inhibitor:  0.133
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.515
CYP2C9-substrate:  0.614
CYP2D6-inhibitor:  0.231
CYP2D6-substrate:  0.296
CYP3A4-inhibitor:  0.092
CYP3A4-substrate:  0.157

ADMET: Excretion

Clearance (CL):  8.874
Half-life (T1/2):  0.953

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.24
Drug-inuced Liver Injury (DILI):  0.929
AMES Toxicity:  0.212
Rat Oral Acute Toxicity:  0.05
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.719
Carcinogencity:  0.329
Eye Corrosion:  0.003
Eye Irritation:  0.056
Respiratory Toxicity:  0.05

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  Natural Product: NPC223548

Natural Product ID:  NPC223548
Common Name*:   JRXLVUMFJASLDR-PXYYCUNGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JRXLVUMFJASLDR-PXYYCUNGSA-N
Standard InCHI:  InChI=1S/C18H17NO6/c20-13-5-1-11(2-6-13)9-14(18(24)25)19-17(23)8-4-12-3-7-15(21)16(22)10-12/h1-8,10,14,20-22H,9H2,(H,19,23)(H,24,25)/b8-4+/t14-/m0/s1
SMILES:  c1cc(ccc1C[C@@H](C(=O)O)N=C(/C=C/c1ccc(c(c1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10308838
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004319] Tyrosine and derivatives

*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
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)00169-2]
NPO4654 Critonia quadrangularis Species Asteraceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)81431-4]
NPO25903 Swinglea glutinosa Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[11575960]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[11975485]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. fruit n.a. PMID[15128023]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[21446699]
NPO16601 Styrax perkinsiae Species Styracaceae Eukaryota n.a. bark n.a. PMID[26762060]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[31763840]
NPO12697 Baccharis megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3437280]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[9748368]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO16289 Marrubium supinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15760 Aconitum pseudohuiliense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10247 Orthosphenia mexicana Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17259 Thuja standishii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9196 Aconitum sachalinense Species Ranunculaceae 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]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15024 Senecio rivularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15147 Ficus simplicissima Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4654 Critonia quadrangularis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14572 Senecio latifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21913 Verbesina rupestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25903 Swinglea glutinosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5468 Dacrydium fonki Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13396 Aplophyllum popovii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16522 Ceratozamia fuscoviridis Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13719 Salacia prinoides Species Sertulariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16601 Styrax perkinsiae Species Styracaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2372 Cryptotermes cynocephalus Species Termitoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16766 Haplophyllum dauricum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16071 Erigeron crispus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16289 Marrubium supinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14413 Bombus muscorum Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12697 Baccharis megapotamica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18873.8 Salmonella enterica subsp. enterica serovar typhimurium Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14723 Streptomyces xantholiticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15531 Quercus dentata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12438 Fomes cajanderi Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7515 Codium decorticatum Species Codiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15760 Aconitum pseudohuiliense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10431 Eupatorium gracile Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10802 Rhinoceros sondaicus Species Rhinocerotidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14892 Flemingia congesta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29175 Strychnos tabascana Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11233 Pseudocyphellaria impressa Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4448 Relhania pumila Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9196 Aconitum sachalinense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16435 Cacalia bicolor Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13872 Amanita cokeri Species Amanitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14046 Stevia mercedensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24501 Asteriscus graveolens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9823 Centrosema pascuorum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11915 Lecanora planaica Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26436 Citrus glauca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13563 Alstonia deplanchei Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16856 Solanum elaeagnifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15969 Alcyonium molle Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10247 Orthosphenia mexicana Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9107 Metalasia bolusii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO576 Oxyanthus speciosus Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17259 Thuja standishii Species Cupressaceae 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
NPT78 Individual Protein Beta amyloid A4 protein Homo sapiens IC50 = 87800.0 nM PMID[547507]

☑ 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 NPC223548 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 NPC223548 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