Structure

Physi-Chem Properties

Molecular Weight:  314.04
Volume:  291.506
LogP:  2.686
LogD:  2.426
LogS:  -3.864
# Rotatable Bonds:  1
TPSA:  113.27
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  4
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.495
Synthetic Accessibility Score:  2.864
Fsp3:  0.062
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.02
MDCK Permeability:  1.5382349374704063e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.914
Human Intestinal Absorption (HIA):  0.093
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  85.8152084350586%
Volume Distribution (VD):  0.966
Pgp-substrate:  18.53287696838379%

ADMET: Metabolism

CYP1A2-inhibitor:  0.973
CYP1A2-substrate:  0.897
CYP2C19-inhibitor:  0.073
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.598
CYP2C9-substrate:  0.834
CYP2D6-inhibitor:  0.36
CYP2D6-substrate:  0.388
CYP3A4-inhibitor:  0.346
CYP3A4-substrate:  0.074

ADMET: Excretion

Clearance (CL):  8.205
Half-life (T1/2):  0.868

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.772
Drug-inuced Liver Injury (DILI):  0.989
AMES Toxicity:  0.106
Rat Oral Acute Toxicity:  0.285
Maximum Recommended Daily Dose:  0.922
Skin Sensitization:  0.859
Carcinogencity:  0.054
Eye Corrosion:  0.354
Eye Irritation:  0.946
Respiratory Toxicity:  0.523

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  Natural Product: NPC184683

Natural Product ID:  NPC184683
Common Name*:   KOIJKAWJZPBTDR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KOIJKAWJZPBTDR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H10O7/c1-21-11-4-7-10(5-8(11)18)22-16-13(7)15(20)14-9(19)2-6(17)3-12(14)23-16/h2-5,17-19H,1H3
SMILES:  COc1cc2c(cc1O)oc1c2c(=O)c2c(cc(cc2o1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   15126297
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002901] Isoflav-2-enes
          • [CHEMONTID:0000494] Isoflavones

*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
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[12964155]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO11789 Swertia decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[16286309]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO733 Pseudoceratina arabica Species Pseudoceratinidae Eukaryota n.a. Red Sea n.a. PMID[18598078]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19191560]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO12644 Lunularia cruciata Species Lunulariaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[23377931]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25620156]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO4734 Syzygium nervosum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[27797185]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO12644 Lunularia cruciata Species Lunulariaceae Eukaryota n.a. n.a. n.a. PMID[30848895]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24178 Citrus rugulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26606 Macadamia ternifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7001 Berberis floribunda Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9452 Pulsatilla campanella Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8701 Bonamia spectabilis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7001 Berberis floribunda Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24178 Citrus rugulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26606 Macadamia ternifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7319 Jamesoniella colorata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11789 Swertia decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26606 Macadamia ternifolia Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9452 Pulsatilla campanella Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11534 Astragalus spinosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3311 Diplacus longiflorus Species Phrymaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12864 Trogoderma granarium Species Dermestidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3658 Achillea pseudopectinata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO733 Pseudoceratina arabica Species Pseudoceratinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11910 Peltogyne pubescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12644 Lunularia cruciata Species Lunulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11223 Pleurotus japonicus Species Pleurotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2280 Streptomyces griseochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18447 Papaver tatricum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23899 Rosulabryum capillare Species Bryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12169 Ranunculus peltatus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3292 Desmodium styracifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4910 Lepidosperma ustulatum Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6572 Dunalia solanacea Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7319 Jamesoniella colorata Species Jungermanniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2565 Aglaia australiensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8701 Bonamia spectabilis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7001 Berberis floribunda Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8398 Cymodocea nodosa Species Cymodoceaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8006 Berlinia tomentosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9640 Dinophysis fortii Species Dinophysiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24178 Citrus rugulosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12284 Hydrangea serrata Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15439 Iyengaria stellata Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7627 Fumaria micrantha Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4734 Syzygium nervosum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9226 Astragalus pycnanthus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7949 Pterodon emarginatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9009 Atuna racemosa Species Chrysobalanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10546 Allagopappus viscosissimus Species Asteraceae 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 NPC184683 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 NPC184683 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