Structure

Physi-Chem Properties

Molecular Weight:  412.37
Volume:  479.432
LogP:  7.529
LogD:  6.457
LogS:  -6.801
# Rotatable Bonds:  5
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.457
Synthetic Accessibility Score:  4.681
Fsp3:  0.862
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.619
MDCK Permeability:  2.0338775357231498e-05
Pgp-inhibitor:  0.431
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.989
30% Bioavailability (F30%):  0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.014
Plasma Protein Binding (PPB):  94.8835678100586%
Volume Distribution (VD):  1.258
Pgp-substrate:  1.7184823751449585%

ADMET: Metabolism

CYP1A2-inhibitor:  0.148
CYP1A2-substrate:  0.401
CYP2C19-inhibitor:  0.107
CYP2C19-substrate:  0.929
CYP2C9-inhibitor:  0.207
CYP2C9-substrate:  0.239
CYP2D6-inhibitor:  0.051
CYP2D6-substrate:  0.883
CYP3A4-inhibitor:  0.766
CYP3A4-substrate:  0.581

ADMET: Excretion

Clearance (CL):  6.987
Half-life (T1/2):  0.03

ADMET: Toxicity

hERG Blockers:  0.13
Human Hepatotoxicity (H-HT):  0.101
Drug-inuced Liver Injury (DILI):  0.364
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.136
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.345
Carcinogencity:  0.034
Eye Corrosion:  0.874
Eye Irritation:  0.249
Respiratory Toxicity:  0.436

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  Natural Product: NPC46213

Natural Product ID:  NPC46213
Common Name*:   RSMKYRDCCSNYFM-AAGDOFLISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RSMKYRDCCSNYFM-AAGDOFLISA-N
Standard InCHI:  InChI=1S/C29H48O/c1-18(2)19(3)8-9-20(4)23-12-13-25-22-10-11-24-21(5)27(30)15-17-29(24,7)26(22)14-16-28(23,25)6/h10,18,20-21,23-27,30H,3,8-9,11-17H2,1-2,4-7H3/t20-,21+,23-,24+,25+,26+,27+,28-,29+/m1/s1
SMILES:  CC(C)C(=C)CC[C@@H](C)[C@H]1CC[C@H]2C3=CC[C@H]4[C@H](C)[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5283640
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003567] Ergostane steroids
          • [CHEMONTID:0001403] Ergosterols 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
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1172/JCI16309]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1371/journal.pone.0115359]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10557354]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11034610]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11419736]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11530998]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1175644]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12391014]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12812989]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12840027]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12878451]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15230696]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15314235]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16112079]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16770722]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1687010]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17116739]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17875433]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18311922]
NPO14304.1 Physalis alkekengi var. franchetii Varieties Solanaceae Eukaryota calyces Yilan, Heilongjiang Province, China 2004-SEP PMID[18348534]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18544912]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18799520]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19425150]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19961175]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota Stems n.a. n.a. PMID[20104880]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20506249]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20601097]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. faeces n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. bile n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. urine n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20876113]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[21798258]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[22342101]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2268561]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[22711758]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23315938]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23717534]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23752203]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23810710]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23811455]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23868375]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23919613]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24101735]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24399466]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24494566]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24558969]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24816727]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25114169]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25181601]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25293588]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25644343]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota aerial parts n.a. n.a. PMID[25895106]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26236990]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27471436]
NPO9585 Oenothera biennis Species Onagraceae Eukaryota Seeds Yichun, Heilongjiang Province, China 2018-Sep PMID[31292343]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3179836]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[347637]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4696527]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[5432584]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6121420]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6780563]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8600370]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8987136]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9192820]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9800648]
NPO9585 Oenothera biennis Species Onagraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9585 Oenothera biennis Species Onagraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO14304.1 Physalis alkekengi var. franchetii Varieties Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11990 Coleostephus myconis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO918 Dahlia pinnata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO11990 Coleostephus myconis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14304.1 Physalis alkekengi var. franchetii Varieties Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO918 Dahlia pinnata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11990 Coleostephus myconis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12934 Gynostemma pentaphyllum Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16506 Synotis alata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9585 Oenothera biennis Species Onagraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO918 Dahlia pinnata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11990 Coleostephus myconis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4305 Pertusaria wulfenii Species Pertusariaceae 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
NPO9585 NPC46213 Other Seed 5.65 3.6 7.7 mg/100g Database [DUKE]

☑ 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 NPC46213 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 NPC46213 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