Structure

Physi-Chem Properties

Molecular Weight:  288.06
Volume:  276.613
LogP:  2.062
LogD:  1.603
LogS:  -3.479
# Rotatable Bonds:  1
TPSA:  107.22
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.599
Synthetic Accessibility Score:  2.971
Fsp3:  0.133
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.451
MDCK Permeability:  5.859755219717044e-06
Pgp-inhibitor:  0.005
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.957
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.012
Plasma Protein Binding (PPB):  97.39130401611328%
Volume Distribution (VD):  0.438
Pgp-substrate:  3.8527309894561768%

ADMET: Metabolism

CYP1A2-inhibitor:  0.442
CYP1A2-substrate:  0.106
CYP2C19-inhibitor:  0.274
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.785
CYP2C9-substrate:  0.809
CYP2D6-inhibitor:  0.469
CYP2D6-substrate:  0.339
CYP3A4-inhibitor:  0.349
CYP3A4-substrate:  0.162

ADMET: Excretion

Clearance (CL):  17.735
Half-life (T1/2):  0.884

ADMET: Toxicity

hERG Blockers:  0.039
Human Hepatotoxicity (H-HT):  0.103
Drug-inuced Liver Injury (DILI):  0.957
AMES Toxicity:  0.313
Rat Oral Acute Toxicity:  0.633
Maximum Recommended Daily Dose:  0.034
Skin Sensitization:  0.947
Carcinogencity:  0.581
Eye Corrosion:  0.003
Eye Irritation:  0.924
Respiratory Toxicity:  0.168

Download Data

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

  Natural Product: NPC119092

Natural Product ID:  NPC119092
Common Name*:   NPLTVGMLNDMOQE-LLVKDONJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NPLTVGMLNDMOQE-LLVKDONJSA-N
Standard InCHI:  InChI=1S/C15H12O6/c16-8-3-1-7(2-4-8)11-5-9(17)13-12(21-11)6-10(18)14(19)15(13)20/h1-4,6,11,16,18-20H,5H2/t11-/m1/s1
SMILES:  c1cc(ccc1[C@H]1CC(=O)c2c(cc(c(c2O)O)O)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones

*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
NPO13968 Garcinia scortechinii Species Clusiaceae Eukaryota fruits n.a. n.a. PMID[16038540]
NPO14358 Rhodobacter sphaeroides Species Rhodobacteraceae Bacteria n.a. n.a. n.a. PMID[1612412]
NPO8068 Blumea mollis Species Asteraceae Eukaryota n.a. leaf n.a. PMID[18566831]
NPO14162 Chlorophytum borivilianum Species Asparagaceae Eukaryota roots n.a. n.a. PMID[19128156]
NPO7016 Gardenia tubifera Species Rubiaceae Eukaryota exudate n.a. n.a. PMID[20028108]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20674349]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. stem n.a. PMID[21428274]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. leaf n.a. PMID[21428274]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[22272932]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25320841]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. fruit n.a. PMID[26169681]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4004 Aquilegia ecalcarata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13968 Garcinia scortechinii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16703 Isodon lophanthoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13766 Ceanothus velutinus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4004 Aquilegia ecalcarata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7016 Gardenia tubifera Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14057 Apollonias barbujana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO205 Lasianthus fordii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16703 Isodon lophanthoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8068 Blumea mollis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11998 Ledebouria socialis Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5191 Penicillium cinerascens Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO746 Panax innovans Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4671 Persea mexicana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10550 Artemisia hanseniana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8892 Sordaria araneosa Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13467 Anarsia lineatella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14358 Rhodobacter sphaeroides Species Rhodobacteraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14162 Chlorophytum borivilianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12509 Dipterocarpus dyeri Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13968 Garcinia scortechinii Species Clusiaceae 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 NPC119092 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 NPC119092 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