Structure

Physi-Chem Properties

Molecular Weight:  112.02
Volume:  104.941
LogP:  1.0
LogD:  0.714
LogS:  -0.688
# Rotatable Bonds:  1
TPSA:  50.44
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.589
Synthetic Accessibility Score:  2.028
Fsp3:  0.0
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:  -4.759
MDCK Permeability:  1.2427962246874813e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.109

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.312
Plasma Protein Binding (PPB):  80.81998443603516%
Volume Distribution (VD):  0.336
Pgp-substrate:  40.090606689453125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.078
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.033
CYP2C9-substrate:  0.121
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.069

ADMET: Excretion

Clearance (CL):  5.05
Half-life (T1/2):  0.911

ADMET: Toxicity

hERG Blockers:  0.061
Human Hepatotoxicity (H-HT):  0.255
Drug-inuced Liver Injury (DILI):  0.754
AMES Toxicity:  0.09
Rat Oral Acute Toxicity:  0.952
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.092
Carcinogencity:  0.793
Eye Corrosion:  0.621
Eye Irritation:  0.996
Respiratory Toxicity:  0.942

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  Natural Product: NPC311988

Natural Product ID:  NPC311988
Common Name*:   SMNDYUVBFMFKNZ-UHFFFAOYSA-M
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SMNDYUVBFMFKNZ-UHFFFAOYSA-M
Standard InCHI:  InChI=1S/C5H4O3/c6-5(7)4-2-1-3-8-4/h1-3H,(H,6,7)/p-1
SMILES:  c1cc(C(=O)[O-])oc1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5460151
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000076] Furans
        • [CHEMONTID:0004758] Furoic acid and derivatives
          • [CHEMONTID:0001448] Furoic acids

*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
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94679-X]
NPO30648 Alisma orientale Species Alismataceae Eukaryota rhizome n.a. n.a. PMID[10560729]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. rhizome n.a. PMID[17541191]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. rhizome n.a. PMID[18787781]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[21302967]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. PMID[21377852]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21574561]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23747095]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO30648 Alisma orientale Species Alismataceae Eukaryota Rhizome n.a. n.a. PMID[26425784]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. tuber n.a. PMID[26666273]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27228227]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota Fruits n.a. n.a. PMID[29140705]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29192771]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[30199256]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[9544564]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Shoot Essent. Oil n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30123 Porphyra tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27048 Pyropia tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO78 Rhizoma homalomenae occultae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14364.1 Alisma plantago-aquatica subsp. orientale Subspecies Alismataceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30123 Porphyra tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14364.1 Alisma plantago-aquatica subsp. orientale Subspecies Alismataceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14364.1 Alisma plantago-aquatica subsp. orientale Subspecies Alismataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27048 Pyropia tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20513 Codium fragile Species Codiaceae 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 NPC311988 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 NPC311988 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