Structure

Physi-Chem Properties

Molecular Weight:  506.27
Volume:  492.047
LogP:  0.63
LogD:  -0.09
LogS:  -2.672
# Rotatable Bonds:  9
TPSA:  178.53
# H-Bond Aceptor:  11
# H-Bond Donor:  7
# Rings:  3
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.189
Synthetic Accessibility Score:  4.947
Fsp3:  0.917
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:  -6.006
MDCK Permeability:  0.00011008478759322315
Pgp-inhibitor:  0.017
Pgp-substrate:  0.903
Human Intestinal Absorption (HIA):  0.823
20% Bioavailability (F20%):  0.788
30% Bioavailability (F30%):  0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.049
Plasma Protein Binding (PPB):  79.689453125%
Volume Distribution (VD):  0.488
Pgp-substrate:  15.85657787322998%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.048
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.315
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.103
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.025

ADMET: Excretion

Clearance (CL):  0.919
Half-life (T1/2):  0.692

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.191
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.365
Rat Oral Acute Toxicity:  0.078
Maximum Recommended Daily Dose:  0.138
Skin Sensitization:  0.781
Carcinogencity:  0.105
Eye Corrosion:  0.003
Eye Irritation:  0.046
Respiratory Toxicity:  0.035

Download Data

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

  Natural Product: NPC1890

Natural Product ID:  NPC1890
Common Name*:   YJLYBYZPMFKXAS-VJQYVDPNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YJLYBYZPMFKXAS-VJQYVDPNSA-N
Standard InCHI:  InChI=1S/C24H42O11/c1-11-7-13(26)8-24(3,4)14(11)6-5-12(2)33-23-21(31)19(29)18(28)16(35-23)10-32-22-20(30)17(27)15(9-25)34-22/h12-13,15-23,25-31H,5-10H2,1-4H3/t12-,13+,15+,16-,17+,18-,19+,20-,21-,22-,23-/m1/s1
SMILES:  CC1=C(CC[C@@H](C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]3[C@@H]([C@H]([C@H](CO)O3)O)O)O2)O)O)O)C(C)(C)C[C@H](C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101843547
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001766] Fatty acyl glycosides
          • [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO24176 Streptomyces fradiae Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[10757717]
NPO2353 Bituminaria bituminosa Species Fabaceae Eukaryota n.a. aerial part n.a. PMID[12943781]
NPO7484 Salacia chinensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[12951446]
NPO7484 Salacia chinensis Species Celastraceae Eukaryota stems Thailand n.a. PMID[14510595]
NPO14555 Porella swartziana Species Porellaceae Eukaryota n.a. Argentine n.a. PMID[14738381]
NPO14555 Porella swartziana Species Porellaceae Eukaryota n.a. n.a. n.a. PMID[14738381]
NPO12977 Solenopsis invicta Species Formicidae Eukaryota n.a. n.a. n.a. PMID[21905650]
NPO23289 Heracleum sphondylium Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24697288]
NPO14826 Streptomyces mobaraensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[32998509]
NPO9420 Aspergillus arenarius Species Aspergillaceae Eukaryota sclerotia n.a. n.a. PMID[9599285]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16847 Consolida ajacis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12416 Quercus mongolica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23289 Heracleum sphondylium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15510 Kummerowia striata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12450 Cneorum pulverulentum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23289 Heracleum sphondylium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12416 Quercus mongolica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14869 Ormosia panamensis Species Limoniidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16847 Consolida ajacis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15510 Kummerowia striata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16847 Consolida ajacis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12416 Quercus mongolica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12977 Solenopsis invicta Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13548 Chrozophora obliqua Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15755 Thymbra spicata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14555 Porella swartziana Species Porellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8499 Osmerus mordax Species Osmeridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5269 Coleus garckeanus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11194 Bombus hortorum Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14034 Salvia coulteri Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7484 Salacia chinensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5552 Solanum sisymbriifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9780 Merremia umbellata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11881 Adenopeltis colliguaya Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16175 Trichia floriformis Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15858 Phoebe formosana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13859 Senecio flavus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14869 Ormosia panamensis Species Limoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13230 Pedicularis condensata Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15015 Meconopsis napaulensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2353 Bituminaria bituminosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11599 Elaeagnus commutata Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5728 Gerbera piloselloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16678 Flindersia brayleyana Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9420 Aspergillus arenarius Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13710 Lyophyllum shimeji Species Lyophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3391 Jungermannia obovata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12450 Cneorum pulverulentum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15272 Mascarenhasia arborescens Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12555 Aspergillus quadrilineatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14826 Streptomyces mobaraensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12680 Perityle vaseyi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12416 Quercus mongolica Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5078 Turraeanthus mannii Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23289 Heracleum sphondylium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15510 Kummerowia striata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15393 Eucalyptus flocktoniae Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15961 Sida cordifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16428 Millettia conraui Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26017 Dalbergia stipulacea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24176 Streptomyces fradiae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13375 Palafoxia rosea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14218 Spodoptera littoralis Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16847 Consolida ajacis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24732 Cereus weberi Species Sagartiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16516 Centaurea seridis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15138 Rheum webbianum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16758 Satureja cuneifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4935 Dinemasporium strigosum Species Chaetosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4267 Ceratocystis clavigera Species Ceratocystidaceae 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 NPC1890 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 NPC1890 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