Structure

Physi-Chem Properties

Molecular Weight:  316.06
Volume:  300.063
LogP:  2.817
LogD:  2.209
LogS:  -3.673
# Rotatable Bonds:  2
TPSA:  120.36
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.535
Synthetic Accessibility Score:  2.535
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.105
MDCK Permeability:  1.0450243280502036e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.865
Human Intestinal Absorption (HIA):  0.132
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.004
Plasma Protein Binding (PPB):  93.30559539794922%
Volume Distribution (VD):  0.644
Pgp-substrate:  10.745466232299805%

ADMET: Metabolism

CYP1A2-inhibitor:  0.966
CYP1A2-substrate:  0.88
CYP2C19-inhibitor:  0.061
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.601
CYP2C9-substrate:  0.797
CYP2D6-inhibitor:  0.409
CYP2D6-substrate:  0.486
CYP3A4-inhibitor:  0.422
CYP3A4-substrate:  0.096

ADMET: Excretion

Clearance (CL):  7.24
Half-life (T1/2):  0.913

ADMET: Toxicity

hERG Blockers:  0.125
Human Hepatotoxicity (H-HT):  0.056
Drug-inuced Liver Injury (DILI):  0.88
AMES Toxicity:  0.372
Rat Oral Acute Toxicity:  0.035
Maximum Recommended Daily Dose:  0.881
Skin Sensitization:  0.946
Carcinogencity:  0.029
Eye Corrosion:  0.008
Eye Irritation:  0.92
Respiratory Toxicity:  0.275

Download Data

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

  Natural Product: NPC1587

Natural Product ID:  NPC1587
Common Name*:   UGPOBASOHYMNAK-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UGPOBASOHYMNAK-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H12O7/c1-22-14-3-7(2-11(20)16(14)21)12-6-10(19)15-9(18)4-8(17)5-13(15)23-12/h2-6,17-18,20-21H,1H3
SMILES:  COc1cc(cc(c1O)O)c1cc(=O)c2c(cc(cc2o1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11267045
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002595] 3'-O-methylated flavonoids

*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
NPO19975 Pycnandra acuminata Species Sapotaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytochem.2007.07.001]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota Artemisia mongolica n.a. n.a. PMID[11087599]
NPO5140 Dipteryx odorata Species Fabaceae Eukaryota seeds n.a. n.a. PMID[12762787]
NPO5140 Dipteryx odorata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[12762809]
NPO6412 Echinacea pallida Species Asteraceae Eukaryota root n.a. n.a. PMID[15921428]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. PMID[29035525]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO633 Mesembryanthemum expansum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20569 Psychotria serpens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5140 Dipteryx odorata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO633 Mesembryanthemum expansum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20569 Psychotria serpens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1252 Aglaia grandis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6856.1 Artemisia ludoviciana subsp. mexicana Subspecies Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5140 Dipteryx odorata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26719 Tetrapanax papyrifer Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20569 Psychotria serpens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11506 Stipa vaseyi Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10536 Rhabdonia verticillata Species Areschougiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO940 Vernonia anisochaetoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10304 Colletotrichum gloeosporioides Species Glomerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6856.1 Artemisia ludoviciana subsp. mexicana Subspecies Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12828 Dysidea tupha Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26719 Tetrapanax papyrifer Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26095 Hypericum revolutum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8609 Hopea utilis Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7779 Impatiens edgeworthii Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1252 Aglaia grandis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20569 Psychotria serpens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12153 Adenia globosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10483 Chrysanthemum sinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5534 Alternaria kikuchiana Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4759 Helleborus multifidus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10798 Cis punctifer Species Ciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO557 Bhesa nitidissima Species Centroplacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12613 Catunaregam tomentosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7968 Artemisia kurramensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10970 Osmorhiza aristata Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19975 Pycnandra acuminata Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8129 Inocybe geophylla Species Inocybaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1695 Monascus pilosus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7463 Ranzania japonica Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11544 Vernonia lanuginosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11452 Pterocarpus officinalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5140 Dipteryx odorata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9447 Tolypothrix tenuis Species Tolypothrichaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7874 Helichrysum lepidissimum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10081 Othonna sedifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5118 Zanthoxylum myriacanthum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11583 Calycanthus floridus Species Calycanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6412 Echinacea pallida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO540 Anaphalis araneosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4322 Scabiosa succisa Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12118 Cleistopholis staudtii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10010 Evernia vulpina Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6861 Galium dasypodum Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9265 Jasonia candicans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11339 Litsea salicifolia Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6802 Rothmannia wittii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO633 Mesembryanthemum expansum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12602 Leuzea centauroides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26396 Coprinopsis atramentaria Species Psathyrellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO218 Acer carpinifolium Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8120 Episcia cupreata Species Gesneriaceae 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 NPC1587 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 NPC1587 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