Structure

Physi-Chem Properties

Molecular Weight:  382.33
Volume:  438.11
LogP:  4.161
LogD:  3.95
LogS:  -2.997
# Rotatable Bonds:  0
TPSA:  6.48
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.487
Synthetic Accessibility Score:  6.13
Fsp3:  0.769
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.112
MDCK Permeability:  2.5888246454996988e-05
Pgp-inhibitor:  0.118
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.595
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.836
Plasma Protein Binding (PPB):  94.9649658203125%
Volume Distribution (VD):  4.776
Pgp-substrate:  3.851193904876709%

ADMET: Metabolism

CYP1A2-inhibitor:  0.059
CYP1A2-substrate:  0.773
CYP2C19-inhibitor:  0.161
CYP2C19-substrate:  0.296
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.06
CYP2D6-inhibitor:  0.995
CYP2D6-substrate:  0.945
CYP3A4-inhibitor:  0.117
CYP3A4-substrate:  0.385

ADMET: Excretion

Clearance (CL):  6.777
Half-life (T1/2):  0.83

ADMET: Toxicity

hERG Blockers:  0.454
Human Hepatotoxicity (H-HT):  0.904
Drug-inuced Liver Injury (DILI):  0.354
AMES Toxicity:  0.158
Rat Oral Acute Toxicity:  0.127
Maximum Recommended Daily Dose:  0.287
Skin Sensitization:  0.953
Carcinogencity:  0.484
Eye Corrosion:  0.004
Eye Irritation:  0.016
Respiratory Toxicity:  0.953

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

  Natural Product: NPC275806

Natural Product ID:  NPC275806
Common Name*:   FXQRSXWMFRVMOS-IVGLGHLBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FXQRSXWMFRVMOS-IVGLGHLBSA-N
Standard InCHI:  InChI=1S/C12H16O4/c1-7(5-8(2)13)10-6-11(15-4)9(3)12(14)16-10/h5-6,8,13H,1-4H3/b7-5+/t8-/m0/s1
SMILES:  C/C(=C[C@H](C)O)/c1cc(c(C)c(=O)o1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   42639813
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives

*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
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. PMID[15568783]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. PMID[19271717]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota Mentha pulegium n.a. n.a. PMID[19271717]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. Caribbean sea n.a. PMID[20727745]
NPO22865 Neopetrosia proxima Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[21341726]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. reef slopes on the south side of Cocos Lagoon, Guam n.a. PMID[21550239]
NPO18542 Salvia sahendica Species Lamiaceae Eukaryota n.a. collected from the plants natural habitat in Tabriz, Northwestern Iran, at an altitude of 1400 m n.a. PMID[21775156]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota Stems n.a. n.a. PMID[23664494]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota isolated from fresh Juncus acutus Lake Wadi el Natrun, Egypt 2012-NOV PMID[25010124]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[25760674]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18279 Paraconiothyrium brasiliense Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18687 Pterocarpus gracilis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18080 Peltophorum ferrugineum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17255 Chondrosia corticata Species Chondrillidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13444 Centaurea ptosimopappoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16860 Stemphylium globuliferum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15888 Streptogonopus phipsoni n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19726 Limnatis nilotica Species Hirudinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18542 Salvia sahendica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18944 Vernonia filigera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19101 Deutzia gracilis Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19382 Corallina elongata Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19321 0tholaena californica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18194 Primula modesta Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14894 Udotea conglutinata Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22865 Neopetrosia proxima Species Petrosiidae 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 NPC275806 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 NPC275806 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