Structure

Physi-Chem Properties

Molecular Weight:  1122.55
Volume:  1062.718
LogP:  0.018
LogD:  0.41
LogS:  -2.773
# Rotatable Bonds:  17
TPSA:  392.59
# H-Bond Aceptor:  25
# H-Bond Donor:  14
# Rings:  9
# Heavy Atoms:  25

MedChem Properties

QED Drug-Likeness Score:  0.053
Synthetic Accessibility Score:  7.008
Fsp3:  0.943
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.55
MDCK Permeability:  0.00048813718603923917
Pgp-inhibitor:  0.007
Pgp-substrate:  0.993
Human Intestinal Absorption (HIA):  0.999
20% Bioavailability (F20%):  0.479
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.083
Plasma Protein Binding (PPB):  41.37211227416992%
Volume Distribution (VD):  -0.106
Pgp-substrate:  22.66754722595215%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.038
CYP2C19-inhibitor:  0.002
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.002
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.035
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  0.217
Half-life (T1/2):  0.808

ADMET: Toxicity

hERG Blockers:  0.514
Human Hepatotoxicity (H-HT):  0.184
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.081
Rat Oral Acute Toxicity:  0.075
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.891
Carcinogencity:  0.165
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.955

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  Natural Product: NPC124834

Natural Product ID:  NPC124834
Common Name*:   UQYNGSPDPASNLN-BLAIOOKWSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UQYNGSPDPASNLN-BLAIOOKWSA-N
Standard InCHI:  InChI=1S/C20H28O7/c1-9-6-12-7-10(2)16(22)15(12)11(3)13(9)4-5-26-20-19(25)18(24)17(23)14(8-21)27-20/h6,10,14,17-21,23-25H,4-5,7-8H2,1-3H3/t10-,14-,17-,18+,19-,20-/m1/s1
SMILES:  Cc1cc2C[C@@H](C)C(=O)c2c(C)c1CCO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   134279
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39770000295]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[10556916]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[10978200]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[11087590]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. PMID[11429258]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota Whole plant n.a. n.a. PMID[18181575]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19406895]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota fruits n.a. n.a. PMID[19902967]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[19917748]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[20932054]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. stem n.a. PMID[23157017]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae Eukaryota n.a. leaf n.a. PMID[23157017]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. Chinese liverworts n.a. PMID[24491225]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25043228]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[25960261]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota stem bark Medicinal Plant Garden, College of Pharmacy, Ewha Womans University 2013-DEC PMID[28787158]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Europe PMC[305622]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[32603106]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. Antarctic n.a. PMID[8882433]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. stem n.a. PMID[8945767]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[9599262]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15818 Lycianthes marlipoensis Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11567 Picradeniopsis absinthifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26770 Pteris multifida Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7056 Pedinophyllum interruptum Species Plagiochilaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29535 Samadera indica Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9155 Kageneckia angustifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11601 Chandonanthus hirtellus Species Anastrophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13360 Passiflora racemosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15094 Coriaria myrtifolia Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12971 Payena lucida Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7868 Xeromphis obovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27659 Tanacetum parthenifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21926 Pseudomonas aeruginosa Species Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO5727 Hymenothrix wislizenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11214 Rivina humilis Species Petiveriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12294 Kydia calycina Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11531 Duguetia calycina Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11785 Citrus hassaku Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10624 Solidago wrightii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12411 Eriostemon spicatus Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1890 Lidbeckia pectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7313 Epirrhoe sperryi Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3494 Swietenia mahagoni Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8866 Papaver atlanticum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12517 Tylophora cordifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8681 Artemisia lactiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2756 Emerita analoga Species Hippidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11032 Coutarea latifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12516 Phalaris canariensis Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14630 Boronia ramosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9835 Catalpa ovata Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2551 Plumbagella micrantha Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13087 Pteridium aquilinum Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8389 Ophryosporus floribundus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12858 Jacaranda chelonia Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13626 Aconitum karakolicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16170 Xerula longipes Species Physalacriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27787 Pseudocentrotus depressus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8611 Cornutia grandifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13236 Viguiera multiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1776 Attalea excelsa Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15726 Rudbeckia subtomentosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7574 Garcinia pyrifera Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2312 Encephalosphaera lasiandra Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO716 Greenwayodendron oliveri Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13121 Crepidiastrum sonchifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15306 Smilax japonica Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12030 Streptomyces yokosukanensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19369 Bacillus thuringiensis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14077 Chamaecyparis lawsoniana Species Cupressaceae 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 80700.0 nM PMID[531651]

☑ 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 NPC124834 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 NPC124834 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