Structure

Physi-Chem Properties

Molecular Weight:  328.05
Volume:  26522078.67
LogP:  -1.546
LogD:  -1.367
LogS:  -0.917
# Rotatable Bonds:  6
TPSA:  116.45
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.436
Synthetic Accessibility Score:  4.668
Fsp3:  1.0
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:  -5.769
MDCK Permeability:  0.00021877720428165048
Pgp-inhibitor:  0.006
Pgp-substrate:  0.973
Human Intestinal Absorption (HIA):  0.841
20% Bioavailability (F20%):  0.6
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.255
Plasma Protein Binding (PPB):  12.703696250915527%
Volume Distribution (VD):  0.787
Pgp-substrate:  86.4615478515625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.079
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.069
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.054
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.12
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  1.164
Half-life (T1/2):  0.667

ADMET: Toxicity

hERG Blockers:  0.045
Human Hepatotoxicity (H-HT):  0.169
Drug-inuced Liver Injury (DILI):  0.034
AMES Toxicity:  0.418
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.825
Skin Sensitization:  0.69
Carcinogencity:  0.185
Eye Corrosion:  0.005
Eye Irritation:  0.769
Respiratory Toxicity:  0.57

Download Data

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

  Natural Product: NPC25916

Natural Product ID:  NPC25916
Common Name*:   GPGHDFGTUWSQOQ-VVULQXIFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GPGHDFGTUWSQOQ-VVULQXIFSA-N
Standard InCHI:  InChI=1S/C10H21AsO7/c1-11(2,16)3-7-8(14)9(15)10(18-7)17-5-6(13)4-12/h6-10,12-15H,3-5H2,1-2H3/t6-,7-,8-,9-,10-/m1/s1
SMILES:  C[As](=O)(C)C[C@@H]1[C@H]([C@H]([C@H](OC[C@@H](CO)O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11198221
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
NPO1482 Gossypium barbadense Species Malvaceae Eukaryota n.a. Zambia; France; West Africa; USA; South Africa n.a. DOI[10.1002/jsfa.2731]
NPO1482 Gossypium barbadense Species Malvaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/ie801365k]
NPO6363 Conyza filaginoides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11374974]
NPO7436 Annona foetida Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[16499336]
NPO1482 Gossypium barbadense Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9493 Lactuca virosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5502 Rhaponticum repens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8652 Onychium japonicum Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9493 Lactuca virosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13596 Lambertella corni-maris Species Rutstroemiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10007 Desmostachya bipinnata Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3899 Spodoptera frugiperda Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7852 Senecio mairetianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6363 Conyza filaginoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8652 Onychium japonicum Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8491 Piper montealegreanum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10260 Tubifera dimorphotheca Species Reticulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5502 Rhaponticum repens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4134 Campanula persicifolia Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1482 Gossypium barbadense Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5615 Dipteryx alata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9875 Primula spectabilis Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1709 Pyrola virens Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8957 Mananthes patentiflora n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7436 Annona foetida Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9493 Lactuca virosa Species Asteraceae 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 NPC25916 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 NPC25916 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