Structure

Physi-Chem Properties

Molecular Weight:  314.08
Volume:  308.569
LogP:  2.568
LogD:  2.199
LogS:  -3.773
# Rotatable Bonds:  3
TPSA:  93.06
# H-Bond Aceptor:  6
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.827
Synthetic Accessibility Score:  3.185
Fsp3:  0.176
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:  -5.266
MDCK Permeability:  1.3549096365750302e-05
Pgp-inhibitor:  0.271
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.021
30% Bioavailability (F30%):  0.545

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.118
Plasma Protein Binding (PPB):  92.45259857177734%
Volume Distribution (VD):  0.611
Pgp-substrate:  7.39670991897583%

ADMET: Metabolism

CYP1A2-inhibitor:  0.687
CYP1A2-substrate:  0.09
CYP2C19-inhibitor:  0.457
CYP2C19-substrate:  0.066
CYP2C9-inhibitor:  0.712
CYP2C9-substrate:  0.866
CYP2D6-inhibitor:  0.9
CYP2D6-substrate:  0.24
CYP3A4-inhibitor:  0.83
CYP3A4-substrate:  0.145

ADMET: Excretion

Clearance (CL):  1.367
Half-life (T1/2):  0.693

ADMET: Toxicity

hERG Blockers:  0.043
Human Hepatotoxicity (H-HT):  0.322
Drug-inuced Liver Injury (DILI):  0.954
AMES Toxicity:  0.315
Rat Oral Acute Toxicity:  0.301
Maximum Recommended Daily Dose:  0.028
Skin Sensitization:  0.156
Carcinogencity:  0.424
Eye Corrosion:  0.004
Eye Irritation:  0.697
Respiratory Toxicity:  0.054

Download Data

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

  Natural Product: NPC153724

Natural Product ID:  NPC153724
Common Name*:   BJYHZSNSMVEQEH-SJORKVTESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BJYHZSNSMVEQEH-SJORKVTESA-N
Standard InCHI:  InChI=1S/C17H14O6/c1-9(18)22-17-15(21)14-12(20)7-11(19)8-13(14)23-16(17)10-5-3-2-4-6-10/h2-8,16-17,19-20H,1H3/t16-,17+/m1/s1
SMILES:  CC(=O)O[C@H]1C(=O)c2c(cc(cc2O[C@@H]1c1ccccc1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   148556
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones
            • [CHEMONTID:0001362] Flavanonols

*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
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[10654416]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. seed n.a. PMID[14577694]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[17548953]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[20014777]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota Aerial parts n.a. n.a. PMID[20166702]
NPO40884 Mexican propolis Species n.a. n.a. n.a. n.a. n.a. PMID[20307087]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. exocarp n.a. PMID[21114277]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. aerial part n.a. PMID[21171571]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. seed n.a. PMID[21942765]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota seeds n.a. n.a. PMID[21942765]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. PMID[22459211]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[24675423]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Enemore, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Gedo, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Holleta, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Bako, Ethiopia PMID[24926420]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. PMID[29094598]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8300 Apis mellifera ligustica Species Apidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10494 Alpinia katsumadai Species Staphylinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14169 Acrocarpia paniculata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9569 Licaria chrysophylla Species Lauraceae 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 NPC153724 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 NPC153724 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