Structure

Physi-Chem Properties

Molecular Weight:  286.11
Volume:  269.914
LogP:  -0.59
LogD:  0.747
LogS:  -1.076
# Rotatable Bonds:  3
TPSA:  119.61
# H-Bond Aceptor:  7
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.477
Synthetic Accessibility Score:  3.582
Fsp3:  0.538
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:  -5.439
MDCK Permeability:  0.0003469803777989
Pgp-inhibitor:  0.0
Pgp-substrate:  0.314
Human Intestinal Absorption (HIA):  0.704
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.812

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.732
Plasma Protein Binding (PPB):  53.38758087158203%
Volume Distribution (VD):  0.768
Pgp-substrate:  46.40168380737305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.072
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.459
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.278
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.278
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.044

ADMET: Excretion

Clearance (CL):  3.253
Half-life (T1/2):  0.653

ADMET: Toxicity

hERG Blockers:  0.042
Human Hepatotoxicity (H-HT):  0.055
Drug-inuced Liver Injury (DILI):  0.084
AMES Toxicity:  0.304
Rat Oral Acute Toxicity:  0.187
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.074
Carcinogencity:  0.39
Eye Corrosion:  0.003
Eye Irritation:  0.025
Respiratory Toxicity:  0.034

Download Data

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

  Natural Product: NPC328055

Natural Product ID:  NPC328055
Common Name*:   YTXIGTCAQNODGD-HENWMNBSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YTXIGTCAQNODGD-HENWMNBSSA-N
Standard InCHI:  InChI=1S/C13H18O7/c1-6-2-7(15)4-8(3-6)19-13-12(18)11(17)10(16)9(5-14)20-13/h2-4,9-18H,5H2,1H3/t9-,10-,11+,12-,13?/m1/s1
SMILES:  CC1=CC(=CC(=C1)OC2C(C(C(C(O2)CO)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   70700401
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:0004165] Phenolic glycosides

*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
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. PMID[20524638]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19963 Curculigo orchioides Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO574 Rumex nepalensis Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19963 Curculigo orchioides Species Hypoxidaceae 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 NPC328055 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 NPC328055 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