Structure

Physi-Chem Properties

Molecular Weight:  474.33
Volume:  511.956
LogP:  5.878
LogD:  6.39
LogS:  -5.16
# Rotatable Bonds:  8
TPSA:  80.67
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.396
Synthetic Accessibility Score:  4.777
Fsp3:  0.897
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.83
MDCK Permeability:  3.46100096066948e-05
Pgp-inhibitor:  0.992
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.048
30% Bioavailability (F30%):  0.808

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.907
Plasma Protein Binding (PPB):  96.06135559082031%
Volume Distribution (VD):  1.094
Pgp-substrate:  1.948077917098999%

ADMET: Metabolism

CYP1A2-inhibitor:  0.057
CYP1A2-substrate:  0.413
CYP2C19-inhibitor:  0.516
CYP2C19-substrate:  0.893
CYP2C9-inhibitor:  0.677
CYP2C9-substrate:  0.059
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.06
CYP3A4-inhibitor:  0.938
CYP3A4-substrate:  0.756

ADMET: Excretion

Clearance (CL):  8.463
Half-life (T1/2):  0.094

ADMET: Toxicity

hERG Blockers:  0.146
Human Hepatotoxicity (H-HT):  0.32
Drug-inuced Liver Injury (DILI):  0.612
AMES Toxicity:  0.027
Rat Oral Acute Toxicity:  0.927
Maximum Recommended Daily Dose:  0.277
Skin Sensitization:  0.173
Carcinogencity:  0.163
Eye Corrosion:  0.59
Eye Irritation:  0.092
Respiratory Toxicity:  0.742

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

  Natural Product: NPC116593

Natural Product ID:  NPC116593
Common Name*:   SGBLZTLTOQYIDO-CZWIXHKBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SGBLZTLTOQYIDO-CZWIXHKBSA-N
Standard InCHI:  InChI=1S/C23H35NO/c1-15(24(4)5)19-8-9-20-18-7-6-16-14-17(25)10-12-22(16,2)21(18)11-13-23(19,20)3/h10,12,14-15,18-21H,6-9,11,13H2,1-5H3/t15-,18-,19+,20-,21-,22-,23+/m0/s1
SMILES:  C[C@@H]([C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)C=C[C@]4(C)[C@H]3CC[C@]12C)N(C)C
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:0003569] Pregnane steroids
          • [CHEMONTID:0001468] Gluco/mineralocorticoids, progestogins 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
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. seed n.a. DOI[10.1007/s11418-005-0009-z]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[11251292]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota stem bark n.a. n.a. PMID[17489632]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. stem n.a. PMID[18484536]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota stem bark Mukono, Uganda 2005-JUN PMID[19008110]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19836230]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20337486]
NPO2713 Xylopia caudata Species Annonaceae Eukaryota Trunk bark the dense rainy forest of Jelebu, in Negeri Sembilan state, Malaysia 2006-FEB PMID[20481544]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21116437]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22026385]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[31125231]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[6875511]
NPO784 Sinapis alba Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2713 Xylopia caudata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8526 Erythrina abyssinica Species Fabaceae 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 NPC116593 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 NPC116593 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