Structure

Physi-Chem Properties

Molecular Weight:  196.07
Volume:  191.655
LogP:  0.529
LogD:  0.673
LogS:  -0.398
# Rotatable Bonds:  1
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.48
Synthetic Accessibility Score:  4.628
Fsp3:  0.5
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:  -4.869
MDCK Permeability:  2.5906983864842914e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.11
20% Bioavailability (F20%):  0.088
30% Bioavailability (F30%):  0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.975
Plasma Protein Binding (PPB):  23.367923736572266%
Volume Distribution (VD):  1.575
Pgp-substrate:  64.18424224853516%

ADMET: Metabolism

CYP1A2-inhibitor:  0.211
CYP1A2-substrate:  0.094
CYP2C19-inhibitor:  0.05
CYP2C19-substrate:  0.436
CYP2C9-inhibitor:  0.042
CYP2C9-substrate:  0.086
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.197
CYP3A4-inhibitor:  0.072
CYP3A4-substrate:  0.255

ADMET: Excretion

Clearance (CL):  3.286
Half-life (T1/2):  0.814

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.125
Drug-inuced Liver Injury (DILI):  0.078
AMES Toxicity:  0.136
Rat Oral Acute Toxicity:  0.808
Maximum Recommended Daily Dose:  0.651
Skin Sensitization:  0.217
Carcinogencity:  0.17
Eye Corrosion:  0.078
Eye Irritation:  0.207
Respiratory Toxicity:  0.651

Download Data

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

  Natural Product: NPC190218

Natural Product ID:  NPC190218
Common Name*:   YMKWNRDVGOVSHY-RBXMUDONSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YMKWNRDVGOVSHY-RBXMUDONSA-N
Standard InCHI:  InChI=1S/C10H12O4/c1-6(11)7-2-3-9-8(13-7)4-5-10(12)14-9/h2-9,11H,1H3/t6-,7-,8+,9+/m0/s1
SMILES:  C[C@@H]([C@@H]1C=C[C@@H]2[C@@H](C=CC(=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:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives
          • [CHEMONTID:0001211] Dihydropyranones

*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]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3124 Gloiopeltis furcata Species Endocladiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5082 Cycas revoluta Species Cycadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1897 Ephedra aphylla Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3419 Quercus suber Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19333 Byssothecium obiones Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7622 Monanchora pulchra Species Crambeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17226 Burkholderia pyrrocinia Species Burkholderiaceae Bacteria 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]
NPO291 Suillus bovinus Species Suillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6850 Typha domingensis Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4293 Allium neapolitanum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10870 Trichilia hirta Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6302 Licaria armeniaca Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25775 Dasystenella acanthina Species Primnoidae 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 NPC190218 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 NPC190218 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