Structure

Physi-Chem Properties

Molecular Weight:  174.05
Volume:  159.75
LogP:  -1.541
LogD:  -1.129
LogS:  -0.307
# Rotatable Bonds:  1
TPSA:  94.83
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.462
Synthetic Accessibility Score:  3.683
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.809
MDCK Permeability:  0.0014441669918596745
Pgp-inhibitor:  0.001
Pgp-substrate:  0.137
Human Intestinal Absorption (HIA):  0.267
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.029

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.845
Plasma Protein Binding (PPB):  19.435766220092773%
Volume Distribution (VD):  0.334
Pgp-substrate:  68.44634246826172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.006
CYP1A2-substrate:  0.047
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.861
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.136
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.007

ADMET: Excretion

Clearance (CL):  3.591
Half-life (T1/2):  0.917

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.133
Drug-inuced Liver Injury (DILI):  0.096
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.047
Carcinogencity:  0.019
Eye Corrosion:  0.006
Eye Irritation:  0.353
Respiratory Toxicity:  0.035

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  Natural Product: NPC267649

Natural Product ID:  NPC267649
Common Name*:   JXOHGGNKMLTUBP-ZLUOBGJFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JXOHGGNKMLTUBP-ZLUOBGJFSA-N
Standard InCHI:  InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/p-1/t4-,5-,6-/m0/s1
SMILES:  C1=C(C[C@@H]([C@H]([C@H]1O)O)O)C(=O)[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10986763
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001292] Cyclic alcohols and derivatives
            • [CHEMONTID:0002509] Cyclitols and derivatives
              • [CHEMONTID:0002278] Shikimic acids and derivatves

*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
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(01)00320-X]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. DOI[10.1078/0176-1617-00195]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[10757735]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. leaf n.a. PMID[11738417]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. stem n.a. PMID[12575075]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[12575075]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[14735439]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[15577255]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. callus n.a. PMID[15715262]
NPO25611 Smilax china Species Smilacaceae Eukaryota stems n.a. n.a. PMID[16252910]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[18220354]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18341288]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO28400 Selaginella pulvinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. PMID[20335035]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. fruit n.a. PMID[21462031]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. PMID[25559759]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. PMID[28445039]
NPO28400 Selaginella pulvinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. PMID[29144743]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota Roots n.a. n.a. PMID[30024167]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30188125]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. PMID[31244143]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Roots n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28400 Selaginella pulvinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28400 Selaginella pulvinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28400 Selaginella pulvinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16931 Cichorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4391 Hypericum perforatum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9865 Cichorium intybus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28400 Selaginella pulvinata Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14158 Selaginella tamariscina Species Selaginellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16931 Cichorium glandulosum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7132 Smilax glabra Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25611 Smilax china Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4391 Hypericum perforatum Species Hypericaceae 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 NPC267649 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 NPC267649 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