Structure

Physi-Chem Properties

Molecular Weight:  374.21
Volume:  388.248
LogP:  3.112
LogD:  2.792
LogS:  -3.547
# Rotatable Bonds:  4
TPSA:  69.67
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.546
Synthetic Accessibility Score:  4.533
Fsp3:  0.773
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.623
MDCK Permeability:  7.456012099282816e-05
Pgp-inhibitor:  0.946
Pgp-substrate:  0.06
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.236
30% Bioavailability (F30%):  0.827

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.876
Plasma Protein Binding (PPB):  51.85599899291992%
Volume Distribution (VD):  0.703
Pgp-substrate:  37.06000518798828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.067
CYP2C19-inhibitor:  0.017
CYP2C19-substrate:  0.317
CYP2C9-inhibitor:  0.034
CYP2C9-substrate:  0.128
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.131
CYP3A4-inhibitor:  0.559
CYP3A4-substrate:  0.289

ADMET: Excretion

Clearance (CL):  2.968
Half-life (T1/2):  0.861

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.098
Drug-inuced Liver Injury (DILI):  0.849
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.101
Maximum Recommended Daily Dose:  0.805
Skin Sensitization:  0.551
Carcinogencity:  0.689
Eye Corrosion:  0.041
Eye Irritation:  0.083
Respiratory Toxicity:  0.634

Download Data

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

  Natural Product: NPC5441

Natural Product ID:  NPC5441
Common Name*:   FAGOJCSZVVRBFD-KAKDVIIHSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FAGOJCSZVVRBFD-KAKDVIIHSA-N
Standard InCHI:  InChI=1S/C22H30O5/c1-12(23)26-19-11-22(3)18(8-9-20(22)27-13(2)24)17-6-4-14-10-15(25)5-7-16(14)21(17)19/h10,16-21H,4-9,11H2,1-3H3/t16-,17-,18+,19+,20-,21-,22-/m0/s1
SMILES:  CC(=O)O[C@@H]1C[C@@]2(C)[C@H](CC[C@@H]2OC(=O)C)[C@@H]2CCC3=CC(=O)CC[C@@H]3[C@H]12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001691] Steroid esters

*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
NPO12029 Sicana odorifera Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[11312792]
NPO15997 Aglaia cordata Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[11754603]
NPO11261 Euclea natalensis Species Ebenaceae Eukaryota root bark n.a. n.a. PMID[15568795]
NPO25076 Salicornia herbacea Species Chenopodiaceae Eukaryota n.a. whole plant n.a. PMID[16276965]
NPO11796 Morus australis Species Moraceae Eukaryota n.a. root n.a. PMID[17405024]
NPO22561 Dickeya chrysanthemi Species Pectobacteriaceae Bacteria n.a. n.a. n.a. PMID[18803373]
NPO25076 Salicornia herbacea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[22652051]
NPO11796 Morus australis Species Moraceae Eukaryota Root Bark n.a. n.a. PMID[27908762]
NPO11796 Morus australis Species Moraceae Eukaryota n.a. n.a. n.a. PMID[9358644]
NPO11796 Morus australis Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13749 Luvunga scandens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14334 Picea jezoensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11796 Morus australis Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13749 Luvunga scandens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15723 Bupleurum aureum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14334 Picea jezoensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15723 Bupleurum aureum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1836 Eupatorium recurvans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12505 Stigmodera macularia Species Buprestidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13749 Luvunga scandens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14893 Streptomyces eurocidicus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14334 Picea jezoensis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15813 Spiraea formosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15302 Acronychia acidula Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22561 Dickeya chrysanthemi Species Pectobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7859 Euonymus atropurpurea Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11261 Euclea natalensis Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13481 Laurencia claviformis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10595 Othonna cylindrica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15903 Goupia tomentosa Species Goupiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13356 Thalictrum fauriei Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16742.1 Syringa pubescens subsp. patula Subspecies Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7047 Psiadia arabica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2740 Pteris plumbea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15997 Aglaia cordata Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25076 Salicornia herbacea Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6038 Acanthamoeba culbertsoni Species Acanthamoebidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13895 Sessibugula translucens n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12805 Othonna intermedia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13232 Gaillardia tontalensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14746 Uroblaniulus canadensis Species Parajulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9145 Herbertus aduncus Species Herbertaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15092 Alternaria infectoria Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14467 Senecio taiwanensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14061 Tetraploa aristata Species Tetraplosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15398 Rhizopus stolonifer Species Rhizopodaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12029 Sicana odorifera Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11796 Morus australis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12291 Rhodococcus ruber Species 0cardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO15628 Strychnos panamensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10093 Castanopsis hystrix Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14205 Uraria picta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11598 Callitris macleayana Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26219 Sorbus coronata Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14873 Pityrodia ternifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8604 Helichrysum zeyheri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15410 Erlangea cordifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9204 Streptomyces argillaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5208 Ligusticum lucidum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4299 Michelia longifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14624 Pertusaria pseudocorallina Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13028 Trichoscypha acuminata Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23600 Bridelia moonii Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1159 Artemisia laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15723 Bupleurum aureum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9541 Suaeda salsa Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27213 Nephrolepis biserrata Species Lomariopsidaceae 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 NPC5441 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 NPC5441 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