Structure

Physi-Chem Properties

Molecular Weight:  316.08
Volume:  284.858
LogP:  -0.539
LogD:  -0.317
LogS:  -1.243
# Rotatable Bonds:  4
TPSA:  156.91
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.38
Synthetic Accessibility Score:  3.464
Fsp3:  0.462
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:  -6.4
MDCK Permeability:  3.9928112528286874e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.06
Human Intestinal Absorption (HIA):  0.719
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.208
Plasma Protein Binding (PPB):  27.489622116088867%
Volume Distribution (VD):  0.298
Pgp-substrate:  61.884220123291016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.067
CYP1A2-substrate:  0.027
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.066
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.111
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  1.731
Half-life (T1/2):  0.923

ADMET: Toxicity

hERG Blockers:  0.134
Human Hepatotoxicity (H-HT):  0.174
Drug-inuced Liver Injury (DILI):  0.86
AMES Toxicity:  0.084
Rat Oral Acute Toxicity:  0.017
Maximum Recommended Daily Dose:  0.001
Skin Sensitization:  0.086
Carcinogencity:  0.028
Eye Corrosion:  0.004
Eye Irritation:  0.174
Respiratory Toxicity:  0.036

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  Natural Product: NPC7753

Natural Product ID:  NPC7753
Common Name*:   ZABGRNGGJZBHDJ-BZNQNGANSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ZABGRNGGJZBHDJ-BZNQNGANSA-N
Standard InCHI:  InChI=1S/C13H16O9/c14-4-8-9(16)10(17)11(18)13(22-8)21-7-3-5(12(19)20)1-2-6(7)15/h1-3,8-11,13-18H,4H2,(H,19,20)/p-1/t8-,9-,10+,11-,13-/m1/s1
SMILES:  c1cc(c(cc1C(=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11972438
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[11076555]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota Roots n.a. n.a. PMID[11459643]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[12880322]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[1517743]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. PMID[21465337]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. bark n.a. PMID[21875098]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[24868863]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[25089845]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[26521454]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27933899]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[28682072]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28960981]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Twigs n.a. n.a. PMID[29883114]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. PMID[8277318]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27772 Flos inulae Species Lycaenidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO243 Ilex chinensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5243 Typha angustata Species Typhaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7422 Hylotelephium mingjinianum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11620 Erica australis Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11620 Erica australis Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO243 Ilex chinensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27772 Flos inulae Species Lycaenidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5243 Typha angustata Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10084 Equisetum hyemale Species Equisetaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7422 Hylotelephium mingjinianum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11620 Erica australis Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7422 Hylotelephium mingjinianum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5243 Typha angustata Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO243 Ilex chinensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18951 Ligusticum sinense Species Apiaceae 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]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10084 Equisetum hyemale Species Equisetaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11391 Polygonum cuspidatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8255 Cinnamomum aromaticum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10084 Equisetum hyemale Species Equisetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29331 Pyrrosia sheareri Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO243 Ilex chinensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7422 Hylotelephium mingjinianum Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11620 Erica australis Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17346 Salvia plebeia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28125 Ephedra equisetina Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5243 Typha angustata Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11391 Polygonum cuspidatum Species Polygonaceae 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 NPC7753 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 NPC7753 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