Structure

Physi-Chem Properties

Molecular Weight:  546.07
Volume:  442.578
LogP:  -2.461
LogD:  -1.329
LogS:  -0.145
# Rotatable Bonds:  8
TPSA:  247.05
# H-Bond Aceptor:  17
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.261
Synthetic Accessibility Score:  5.815
Fsp3:  0.688
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.253
MDCK Permeability:  0.0001378228043904528
Pgp-inhibitor:  0.0
Pgp-substrate:  0.721
Human Intestinal Absorption (HIA):  0.68
20% Bioavailability (F20%):  0.955
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.456
Plasma Protein Binding (PPB):  14.649682998657227%
Volume Distribution (VD):  0.33
Pgp-substrate:  68.67257690429688%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.062
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.029
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.169
CYP2D6-inhibitor:  0.028
CYP2D6-substrate:  0.065
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  1.81
Half-life (T1/2):  0.92

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.423
Drug-inuced Liver Injury (DILI):  0.987
AMES Toxicity:  0.254
Rat Oral Acute Toxicity:  0.008
Maximum Recommended Daily Dose:  0.917
Skin Sensitization:  0.244
Carcinogencity:  0.268
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.299

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Similar NPs/Drugs  

  Natural Product: NPC50864

Natural Product ID:  NPC50864
Common Name*:   VQSYXVWEZATIHL-UHFFFAOYSA-O
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  VQSYXVWEZATIHL-UHFFFAOYSA-O
Standard InCHI:  InChI=1S/C20H19NO4/c1-23-18-9-13-6-7-21-11-15-12(4-5-17(22)20(15)25-3)8-16(21)14(13)10-19(18)24-2/h4-5,8-11H,6-7H2,1-3H3/p+1
SMILES:  COc1cc2CCN3=CC4=C(C(=[OH+])C=CC4=CC=3c2cc1OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   3083983
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001909] Protoberberine alkaloids 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
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. stem wood n.a. DOI[10.1021/np100247r]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10395501]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10425140]
NPO29471 Achyrocline satureioides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11858757]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. PMID[12081149]
NPO21709 Pinus ponderosa Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[12371811]
NPO6333 Annona glabra Species Annonaceae Eukaryota Fruits n.a. n.a. PMID[15568797]
NPO22979 Hildegardia barteri Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[16378378]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. root n.a. PMID[17340259]
NPO25345 Corydalis ternata Species Papaveraceae Eukaryota tubers n.a. n.a. PMID[20594848]
NPO6333 Annona glabra Species Annonaceae Eukaryota stem Taipei Botanical Garden, Taipei, Taiwan, China 2006-MAR PMID[20828184]
NPO18288 Macaranga bicolor Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[21275386]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. root n.a. PMID[22051934]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[22737858]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[23194502]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota aerial parts herbal garden of Chungbuk National University, Cheongju, Korea 2012-Oct PMID[24963714]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. rhizome n.a. PMID[25277281]
NPO6333 Annona glabra Species Annonaceae Eukaryota fruits n.a. n.a. PMID[25499882]
NPO29471 Achyrocline satureioides Species Asteraceae Eukaryota aerial parts Alpa Corral, Cordoba, Argentina 2008-Aug PMID[25517209]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. tuber n.a. PMID[25670016]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. PMID[28836430]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[32058719]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[9584397]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[9599260]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. aerial part n.a. Database[Article]
NPO24050 Stephania glabra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10461 Corydalis adunca Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28638 Corydalis longicalcarata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28372.1 Corydalis pallida var. tenuis Varieties Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28372.1 Corydalis pallida var. tenuis Varieties Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24050 Stephania glabra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28638 Corydalis longicalcarata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10461 Corydalis adunca Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24050 Stephania glabra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25734 Tinospora sagittata Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25345 Corydalis ternata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23024 Epimedium koreanum Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23282 Russula paludosa Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22184 Pseudocyphellaria amphisticta Species Lobariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10008 Tinospora capillipes Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24050 Stephania glabra Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20153 Quercus pontica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6333 Annona glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18288 Macaranga bicolor Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24365 Hymenoxys ivesiana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29471 Achyrocline satureioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1327 Heliothis maritima Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25345 Corydalis ternata Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21709 Pinus ponderosa Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21821 Aeschynomene indica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19027 Passiflora coccinea Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22979 Hildegardia barteri Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO827 Corydalis yanhusuo Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23461 Medicago hispida Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23550 Maytenus octogona Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24183 Brickellia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13528 Funneliformis mosseae Species Glomeraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13962 Corydalis turtschaninovii Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22738 Horsfieldia iryaghedhi Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23885 Agathosma bisulca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23414 Karwinskia subcordata Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22598 Galium lovcense Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25734 Tinospora sagittata Species Menispermaceae 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 NPC50864 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 NPC50864 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