Structure

Physi-Chem Properties

Molecular Weight:  295.11
Volume:  278.223
LogP:  0.18
LogD:  0.075
LogS:  -1.972
# Rotatable Bonds:  3
TPSA:  115.17
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.514
Synthetic Accessibility Score:  3.514
Fsp3:  0.429
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.38
MDCK Permeability:  8.01086389401462e-06
Pgp-inhibitor:  0.004
Pgp-substrate:  0.023
Human Intestinal Absorption (HIA):  0.403
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.712

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.381
Plasma Protein Binding (PPB):  52.853675842285156%
Volume Distribution (VD):  0.609
Pgp-substrate:  35.92909240722656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.176
CYP1A2-substrate:  0.08
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.511
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.703
CYP2D6-inhibitor:  0.047
CYP2D6-substrate:  0.38
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.045

ADMET: Excretion

Clearance (CL):  2.083
Half-life (T1/2):  0.87

ADMET: Toxicity

hERG Blockers:  0.045
Human Hepatotoxicity (H-HT):  0.087
Drug-inuced Liver Injury (DILI):  0.335
AMES Toxicity:  0.363
Rat Oral Acute Toxicity:  0.548
Maximum Recommended Daily Dose:  0.005
Skin Sensitization:  0.442
Carcinogencity:  0.078
Eye Corrosion:  0.005
Eye Irritation:  0.261
Respiratory Toxicity:  0.179

Download Data

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

  Natural Product: NPC254416

Natural Product ID:  NPC254416
Common Name*:   XVARCVCWNFACQC-RKQHYHRCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XVARCVCWNFACQC-RKQHYHRCSA-N
Standard InCHI:  InChI=1S/C14H17NO6/c16-6-10-11(17)12(18)13(19)14(21-10)20-9-5-15-8-4-2-1-3-7(8)9/h1-5,10-19H,6H2/t10-,11-,12+,13-,14-/m1/s1
SMILES:  c1ccc2c(c1)c(c[nH]2)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   441564
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/cbdv.200490123]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[11678654]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15787451]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota Roots Anhui, China n.a. PMID[22694318]
NPO8274 Geijera parviflora Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[23848189]
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[24684844]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[26434122]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO4708 Erythrina lysistemon Species Fabaceae Eukaryota n.a. root n.a. PMID[9170286]
NPO4708 Erythrina lysistemon Species Fabaceae Eukaryota n.a. aerial part n.a. Database[Article]
NPO4708 Erythrina lysistemon Species Fabaceae Eukaryota n.a. flower n.a. Database[Article]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4708 Erythrina lysistemon Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1007 Crotalaria paniculata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31050 Isatis indigotica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23903 Senecio glanduloso-pilosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15101 Tricholoma panaeolum Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6826 Persicaria perfoliata Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18730 Aspidosperma discolor Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8274 Geijera parviflora Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22457 Swertia calycina Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4708 Erythrina lysistemon Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23820 Indigofera suffruticosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4582 Baphicacanthus cusia Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1007 Crotalaria paniculata Species Fabaceae 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 NPC254416 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 NPC254416 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