Structure

Physi-Chem Properties

Molecular Weight:  152.03
Volume:  145.636
LogP:  1.329
LogD:  1.379
LogS:  -2.277
# Rotatable Bonds:  1
TPSA:  35.53
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.567
Synthetic Accessibility Score:  3.59
Fsp3:  0.125
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.53
MDCK Permeability:  2.3154960217652842e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.057

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.914
Plasma Protein Binding (PPB):  85.814453125%
Volume Distribution (VD):  1.597
Pgp-substrate:  11.468897819519043%

ADMET: Metabolism

CYP1A2-inhibitor:  0.993
CYP1A2-substrate:  0.237
CYP2C19-inhibitor:  0.588
CYP2C19-substrate:  0.342
CYP2C9-inhibitor:  0.096
CYP2C9-substrate:  0.758
CYP2D6-inhibitor:  0.779
CYP2D6-substrate:  0.562
CYP3A4-inhibitor:  0.498
CYP3A4-substrate:  0.188

ADMET: Excretion

Clearance (CL):  11.23
Half-life (T1/2):  0.666

ADMET: Toxicity

hERG Blockers:  0.055
Human Hepatotoxicity (H-HT):  0.029
Drug-inuced Liver Injury (DILI):  0.043
AMES Toxicity:  0.049
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.034
Skin Sensitization:  0.415
Carcinogencity:  0.927
Eye Corrosion:  0.95
Eye Irritation:  0.987
Respiratory Toxicity:  0.971

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

  Natural Product: NPC53993

Natural Product ID:  NPC53993
Common Name*:   SATCULPHIDQDRE-DOMIDYPGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SATCULPHIDQDRE-DOMIDYPGSA-N
Standard InCHI:  InChI=1S/C8H6O3/c9-4-6-1-2-7-8(3-6)11-5-10-7/h1-4H,5H2/i4+2
SMILES:  c1cc2c(cc1[14CH]=O)OCO2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10820744
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000296] Benzodioxoles

*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
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4039(01)00209-X]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[10575373]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[11551759]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. leaf n.a. PMID[15467205]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[16808005]
NPO12933 Gymnadenia conopsea Species Orchidaceae Eukaryota tubers n.a. n.a. PMID[18348533]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[20209910]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. whole plant n.a. PMID[21214467]
NPO12933 Gymnadenia conopsea Species Orchidaceae Eukaryota n.a. tuber n.a. PMID[21322946]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23102654]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[31103896]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12933 Gymnadenia conopsea Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31578 Vanilla sp Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12933 Gymnadenia conopsea Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13223 Vanilla sp. Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3634 Robinia pseudoacacia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10742 Galium verum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12933 Gymnadenia conopsea Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28928 Piper nigrum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3634 Robinia pseudoacacia 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 NPC53993 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 NPC53993 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