Structure

Physi-Chem Properties

Molecular Weight:  206.0
Volume:  168.435
LogP:  -0.277
LogD:  -0.228
LogS:  -0.232
# Rotatable Bonds:  4
TPSA:  93.81
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.58
Synthetic Accessibility Score:  4.677
Fsp3:  0.167
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.26
MDCK Permeability:  4.552828977466561e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.22
20% Bioavailability (F20%):  0.103
30% Bioavailability (F30%):  0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.814
Plasma Protein Binding (PPB):  59.35142135620117%
Volume Distribution (VD):  0.608
Pgp-substrate:  62.46859359741211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.021
CYP1A2-substrate:  0.076
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.046
CYP2C9-inhibitor:  0.012
CYP2C9-substrate:  0.292
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.182
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.058

ADMET: Excretion

Clearance (CL):  1.473
Half-life (T1/2):  0.907

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.065
Drug-inuced Liver Injury (DILI):  0.09
AMES Toxicity:  0.039
Rat Oral Acute Toxicity:  0.081
Maximum Recommended Daily Dose:  0.78
Skin Sensitization:  0.301
Carcinogencity:  0.213
Eye Corrosion:  0.937
Eye Irritation:  0.979
Respiratory Toxicity:  0.712

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Similar NPs/Drugs  

  Natural Product: NPC39927

Natural Product ID:  NPC39927
Common Name*:   XUMMAWMKFFMZAH-UHFFFAOYSA-L
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XUMMAWMKFFMZAH-UHFFFAOYSA-L
Standard InCHI:  InChI=1S/C6H7O6P/c7-2-6-1-5(3-11-6)4-12-13(8,9)10/h1-3H,4H2,(H2,8,9,10)/p-2
SMILES:  c1c(coc1C=O)COP(=O)([O-])[O-]
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   25201088
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000124] Aldehydes
            • [CHEMONTID:0003213] Aryl-aldehydes

*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
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1002/elan.200403102]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2012.02.124]
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]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[11077184]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[17328234]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. rhizome n.a. PMID[17541191]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[18321056]
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]
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]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower n.a. PMID[21804227]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota flower buds Henan province, China 2005-MAY PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower bud n.a. PMID[21942812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[23265495]
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]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[24279769]
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 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]
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]
NPO8367 Fructus schiandrae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26605 Funtumia elastica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18681 Artemisia scoparia 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]
NPO5665 Ulva pertusa Species Ulvaceae 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]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25645 Flos lonicerae Species Lycaenidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12656 Holarrhena febrifuga Species Apocynaceae 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]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8367 Fructus schiandrae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16087 Atractylodes lancea Species Asteraceae 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]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12656 Holarrhena febrifuga Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26605 Funtumia elastica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25645 Flos lonicerae Species Lycaenidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27048 Pyropia tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30123 Porphyra tenera Species Bangiaceae 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]
NPO20513 Codium fragile Species Codiaceae 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]
NPO22104 Trifolium pratense Species Fabaceae 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]
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]
NPO1515 Lonicera japonica Species Caprifoliaceae 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]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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[TM-MC]
NPO27018 Cynomorium songaricum Species Cynomoriaceae 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]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5665 Ulva pertusa Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22104 Trifolium pratense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12656 Holarrhena febrifuga Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27048 Pyropia tenera Species Bangiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16087 Atractylodes lancea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14364.1 Alisma plantago-aquatica subsp. orientale Subspecies Alismataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12588 Cornus officinalis Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20414 Ocimum basilicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26605 Funtumia elastica Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1515 Lonicera japonica Species Caprifoliaceae 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 NPC39927 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 NPC39927 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