Structure

Physi-Chem Properties

Molecular Weight:  198.09
Volume:  194.291
LogP:  0.778
LogD:  0.86
LogS:  -0.873
# Rotatable Bonds:  2
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.515
Synthetic Accessibility Score:  4.463
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.693
MDCK Permeability:  8.654187695356086e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.026
Human Intestinal Absorption (HIA):  0.028
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.818

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.88
Plasma Protein Binding (PPB):  22.2518253326416%
Volume Distribution (VD):  1.634
Pgp-substrate:  58.56012725830078%

ADMET: Metabolism

CYP1A2-inhibitor:  0.124
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.041
CYP2C19-substrate:  0.27
CYP2C9-inhibitor:  0.017
CYP2C9-substrate:  0.194
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.192
CYP3A4-inhibitor:  0.055
CYP3A4-substrate:  0.245

ADMET: Excretion

Clearance (CL):  4.835
Half-life (T1/2):  0.86

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.548
Drug-inuced Liver Injury (DILI):  0.354
AMES Toxicity:  0.251
Rat Oral Acute Toxicity:  0.176
Maximum Recommended Daily Dose:  0.038
Skin Sensitization:  0.199
Carcinogencity:  0.198
Eye Corrosion:  0.06
Eye Irritation:  0.311
Respiratory Toxicity:  0.085

Download Data

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

  Natural Product: NPC100433

Natural Product ID:  NPC100433
Common Name*:   SJSGYYGIRSKXTM-RBXMUDONSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SJSGYYGIRSKXTM-RBXMUDONSA-N
Standard InCHI:  InChI=1S/C10H14O4/c1-6(11)7-2-3-8(13-7)9-4-5-10(12)14-9/h2-3,6-9,11H,4-5H2,1H3/t6-,7-,8+,9+/m0/s1
SMILES:  C[C@@H]([C@@H]1C=C[C@H]([C@H]2CCC(=O)O2)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

*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
NPO6850 Typha domingensis Species Typhaceae Eukaryota n.a. aerial part n.a. PMID[21417376]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. n.a. n.a. PMID[21848268]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. Urup Island (4557,9 N; 15044,9 E; depth 66 m) 2008-AUG PMID[21848268]
NPO17226 Burkholderia pyrrocinia Species Burkholderiaceae Bacteria n.a. n.a. n.a. PMID[4955234]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6302 Licaria armeniaca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10870 Trichilia hirta Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25775 Dasystenella acanthina Species Primnoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1897 Ephedra aphylla Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19333 Byssothecium obiones Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3419 Quercus suber Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17226 Burkholderia pyrrocinia Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2968 Anthopleura xanthogrammica Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3756 Munronia delavayi Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2609 Neonectria candida Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO115 Eutreptia viridis Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6130 Mammillaria magnimamma Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4816 Cycas armstrongii Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18463 Plectocephalus chilensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6850 Typha domingensis Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO291 Suillus bovinus Species Suillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4293 Allium neapolitanum Species Amaryllidaceae 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 NPC100433 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 NPC100433 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