Structure

Physi-Chem Properties

Molecular Weight:  286.08
Volume:  291.039
LogP:  3.528
LogD:  2.154
LogS:  -3.816
# Rotatable Bonds:  5
TPSA:  86.99
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.446
Synthetic Accessibility Score:  2.558
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.883
MDCK Permeability:  1.4660769920737948e-05
Pgp-inhibitor:  0.024
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.987
30% Bioavailability (F30%):  0.953

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.015
Plasma Protein Binding (PPB):  100.13402557373047%
Volume Distribution (VD):  0.421
Pgp-substrate:  1.0525212287902832%

ADMET: Metabolism

CYP1A2-inhibitor:  0.752
CYP1A2-substrate:  0.093
CYP2C19-inhibitor:  0.353
CYP2C19-substrate:  0.064
CYP2C9-inhibitor:  0.695
CYP2C9-substrate:  0.47
CYP2D6-inhibitor:  0.585
CYP2D6-substrate:  0.415
CYP3A4-inhibitor:  0.246
CYP3A4-substrate:  0.206

ADMET: Excretion

Clearance (CL):  6.915
Half-life (T1/2):  0.906

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.013
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.276
Rat Oral Acute Toxicity:  0.541
Maximum Recommended Daily Dose:  0.853
Skin Sensitization:  0.932
Carcinogencity:  0.891
Eye Corrosion:  0.006
Eye Irritation:  0.924
Respiratory Toxicity:  0.945

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  Natural Product: NPC138466

Natural Product ID:  NPC138466
Common Name*:   RHHDLPUNPYIFOT-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RHHDLPUNPYIFOT-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H14O5/c1-2-3-10-4-6-12(7-5-10)21-13-8-11(9-17)14(18)16(20)15(13)19/h2,4-9,18-20H,1,3H2
SMILES:  C=CCc1ccc(cc1)Oc1cc(C=O)c(c(c1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   71812224
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0004155] Diphenylethers

*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
NPO15299 Sandoricum koetjape Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[10479314]
NPO12483 Holarrhena floribunda Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[10650079]
NPO15299 Sandoricum koetjape Species Meliaceae Eukaryota stems n.a. n.a. PMID[1517737]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. aerial part n.a. PMID[15577228]
NPO13465 Salvia broussonetii Species Lamiaceae Eukaryota roots n.a. n.a. PMID[15969497]
NPO12483 Holarrhena floribunda Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[16441070]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. stem n.a. PMID[18175990]
NPO12483 Holarrhena floribunda Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. PMID[22085682]
NPO15299 Sandoricum koetjape Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[22672802]
NPO13745 Gynoxys verrucosa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27057812]
NPO15190 Chloranthus fortunei Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[27997206]
NPO6698 Euphorbia pithyusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[28671832]
NPO8583 Angelica japonica Species Apiaceae Eukaryota n.a. root n.a. PMID[9987830]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO10532 Pinus edulis Species Pinaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10532 Pinus edulis Species Pinaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13018 Thelephora aurantiotincta Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12483 Holarrhena floribunda Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8583 Angelica japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13228 Farfugium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13228 Farfugium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9133 Lathyrus latifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12483 Holarrhena floribunda Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8583 Angelica japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15299 Sandoricum koetjape Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3482 Alpinia flabellata Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13018 Thelephora aurantiotincta Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13228 Farfugium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17166 Euphorbia palustris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9133 Lathyrus latifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11246 Ononis viscosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13228 Farfugium japonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25118 Centaurea benedicta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14455 Triunia erythrocarpa Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14329 Sigillina signifera Species Polycitoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18026 Bipolaris sacchari Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2568 Posidonia oceanica Species Posidoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15405 Suaeda maritima Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17336 Benincasa hispida Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9133 Lathyrus latifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8583 Angelica japonica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13018 Thelephora aurantiotincta Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17166 Euphorbia palustris Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13617 Eria rigida Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12018 Alternaria bataticola Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3482 Alpinia flabellata Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11592 Cuphea hyssopifolia Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12483 Holarrhena floribunda Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4282 Fouquieria diguetii Species Fouquieriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13465 Salvia broussonetii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2043 Pseudocyphellaria coronata Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2680 Holothuria squamifera Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9538 Pterocarpus erinaceus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10905 Baccharis truncata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7009 Callyspongia spinosissima Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7844 Fritillaria hupehensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11791 Magnolia obovata Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2070 Thioalkalivibrio versutus Species Ectothiorhodospiraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15992 Hypogymnia vittata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13353 Sedum sarmentosum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17358 Sorbus torminalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15190 Chloranthus fortunei Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14194 Mamestra brassicae Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10048 Pyrus bourgaeana Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10532 Pinus edulis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8721 Parectatosoma mocquerysi Species Anisacanthidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15299 Sandoricum koetjape Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27148 Chuquiraga erinacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13745 Gynoxys verrucosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6698 Euphorbia pithyusa Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO273 Phyllobates bicolor Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5998 Echinoclathria subhispida Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15514 Pedicularis rex Species Orobanchaceae 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 NPC138466 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 NPC138466 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