Structure

Physi-Chem Properties

Molecular Weight:  88.09
Volume:  103.827
LogP:  1.27
LogD:  1.152
LogS:  -0.443
# Rotatable Bonds:  2
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.537
Synthetic Accessibility Score:  2.667
Fsp3:  1.0
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:  -4.186
MDCK Permeability:  3.02058851957554e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.514
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.088
30% Bioavailability (F30%):  0.218

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.84
Plasma Protein Binding (PPB):  20.818239212036133%
Volume Distribution (VD):  1.152
Pgp-substrate:  74.40486145019531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.439
CYP1A2-substrate:  0.866
CYP2C19-inhibitor:  0.063
CYP2C19-substrate:  0.835
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.786
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.458
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.175

ADMET: Excretion

Clearance (CL):  10.226
Half-life (T1/2):  0.781

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.033
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.042
Maximum Recommended Daily Dose:  0.04
Skin Sensitization:  0.165
Carcinogencity:  0.323
Eye Corrosion:  0.984
Eye Irritation:  0.994
Respiratory Toxicity:  0.048

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  Natural Product: NPC158857

Natural Product ID:  NPC158857
Common Name*:   JYVLIDXNZAXMDK-YFKPBYRVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  JYVLIDXNZAXMDK-YFKPBYRVSA-N
Standard InCHI:  InChI=1S/C5H12O/c1-3-4-5(2)6/h5-6H,3-4H2,1-2H3/t5-/m0/s1
SMILES:  CCC[C@H](C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   2724896
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols

*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
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/hlca.19270100148]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1039/C39730000707]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[11473412]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Petals n.a. n.a. PMID[15043425]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. root n.a. PMID[15730255]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[15730255]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[16724861]
NPO26211 Knightia excelsa Species Proteaceae Eukaryota n.a. n.a. n.a. PMID[17315967]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18491868]
NPO26507 Galenia africana Species Aizoaceae Eukaryota leaf n.a. n.a. PMID[20035557]
NPO26654 Penicillium citreonigrum Species Aspergillaceae Eukaryota n.a. atlantic-forest-soil n.a. PMID[20450206]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[21302965]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[24338885]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26566007]
NPO26451 Ophiocoma scolopendrina Species Ophiocomidae Eukaryota n.a. n.a. n.a. PMID[27684202]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[7288445]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO9445 Crocus sativus Species Iridaceae Eukaryota Silk Stigma Style n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota Fruits n.a. Database[FooDB]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26349 Frullania tamarisci Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26699 Leonurus glaucescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25972 Eupolyphaga sinensis Species Corydiidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26211 Knightia excelsa Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26287 Spodoptera eridania Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5510 Lepidium draba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26699 Leonurus glaucescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26561 Micromeria pineolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25949 Streptomyces griseovariabilis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO26406 Saussurea carthamoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26349 Frullania tamarisci Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26052 Swertia delavayi Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26900 Vallota purpurea n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25739 Erysimum odoratum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9445 Crocus sativus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26624 Ilex amara Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26834 Eutypella scoparia Species Diatrypaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26654 Penicillium citreonigrum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25972 Eupolyphaga sinensis Species Corydiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26023 Angelica tarokoensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26184 Diphasia angolensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25792 Delphinium andersoni Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26950 Maba buxifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26584 Gnidia lamprantha Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25769 Heterotheca inuloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26319 Solanum acaule Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25896 Bragantia wallichii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO26134 Epimedium davidii Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26161 Globba malaccensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26374 Alangium premnifolium Species Cornaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2898 Quercus sessiliflora Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26806 Nidula candida Species Nidulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26451 Ophiocoma scolopendrina Species Ophiocomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25995 Laurencia distichophylla Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25870 Vaccinium vitis-idaea Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7447 Nemalion vermiculare Species Liagoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26927 Salacia madagascariensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26507 Galenia africana Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26266 Isodon japonicus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26607 Colobocentrotus atratus Species Echinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25923 Vismia jefensis 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 NPC158857 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 NPC158857 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