Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  251.53
LogP:  4.778
LogD:  4.242
LogS:  -4.708
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.477
Synthetic Accessibility Score:  3.616
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.62
MDCK Permeability:  2.441746437398251e-05
Pgp-inhibitor:  0.721
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.977
30% Bioavailability (F30%):  0.196

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.306
Plasma Protein Binding (PPB):  98.59041595458984%
Volume Distribution (VD):  4.363
Pgp-substrate:  1.1203527450561523%

ADMET: Metabolism

CYP1A2-inhibitor:  0.696
CYP1A2-substrate:  0.505
CYP2C19-inhibitor:  0.346
CYP2C19-substrate:  0.439
CYP2C9-inhibitor:  0.538
CYP2C9-substrate:  0.932
CYP2D6-inhibitor:  0.205
CYP2D6-substrate:  0.631
CYP3A4-inhibitor:  0.115
CYP3A4-substrate:  0.201

ADMET: Excretion

Clearance (CL):  8.041
Half-life (T1/2):  0.689

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.083
Drug-inuced Liver Injury (DILI):  0.035
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.159
Skin Sensitization:  0.925
Carcinogencity:  0.074
Eye Corrosion:  0.391
Eye Irritation:  0.97
Respiratory Toxicity:  0.011

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  Natural Product: NPC94721

Natural Product ID:  NPC94721
Common Name*:   GXEGJTGWYVZSNR-LBJJKJHXSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GXEGJTGWYVZSNR-LBJJKJHXSA-N
Standard InCHI:  InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h6,9H,5,7-8,10-11H2,1-4H3/b13-6-,14-9+
SMILES:  CC(=C1CC/C(=CCC/C(=C/C1)/C)/C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5371080
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane sesquiterpenoids

*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
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1007/s11746-010-1670-2]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.foodcont.2016.09.002]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.jfca.2010.08.006]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2010.06.003]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2010.12.007]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2016.02.010]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2018.06.017]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.12691/jfnr-2-5-9]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[12628396]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[15217296]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. whole plant n.a. PMID[16079548]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[16499319]
NPO13478 Scorzonera pseudodivaricata Species Asteraceae Eukaryota n.a. Mongolian n.a. PMID[17542634]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. sand-covered bottom at -10 to -15 m at Hurghada, on the Egyptian Red Sea coast 2003-JUN PMID[18298079]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. PMID[18942825]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota Hairy roots n.a. n.a. PMID[19271765]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[19628108]
NPO5489 Cinnamomum tenuifolium Species Lauraceae Eukaryota stems n.a. n.a. PMID[19754130]
NPO12855 Alkanna cappadocica Species Boraginaceae Eukaryota n.a. n.a. n.a. PMID[20405844]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[22538527]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. leaf n.a. PMID[24024688]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[24811150]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. fruit n.a. PMID[25522543]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26285573]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[28274428]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30236698]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds Guangzhou, China PMID[30563201]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30583361]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30599958]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[31159190]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[31861466]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6619887]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[6631435]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264679]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7264682]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[7320741]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. n.a. PMID[7798960]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24390.1 Juniperus rigida var. conferta Varieties Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1834 Atalantia racemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11848 Lemaireocereus griseus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13671 Ononis vaginalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5930 Crambe tatarica Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3492 Negombata magnifica Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9919 Jaspis stellifera Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29494 Stoeba extensa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24390.1 Juniperus rigida var. conferta Varieties Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8928 Pteris semipinnata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12196 Buphane fischeri n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2236 Pyrola rotundifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9934 Mycobacterium leprae Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1834 Atalantia racemosa Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9313 Fritillaria ningguoensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10783 Syncarpia hillii Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13585 Rapanea lancifolia Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2398 Millettia erythrocalyx Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11021 Moringa oleifera Species Moringaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5881 Catharanthus roseus Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17324 Pluchea dioscoridis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11107 Stevia alpina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13030 Artemisia dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7263 Phyllobates aurotaenia Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21830 Buddleja cordata Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7003 Streptomyces violaceochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO13478 Scorzonera pseudodivaricata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12855 Alkanna cappadocica Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8528 Citrus junos Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13857 Mentha canadensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12700 Diospyros eriantha Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO252 Hoffmannia strigillosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9765 Petriella guttulata Species Microascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4311 Asterolasia squamuligera Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23256 Mentha arvensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5489 Cinnamomum tenuifolium Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10402 Strophanthus eminii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14578 Prorocentrum micans Species Prorocentraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6360 Xenoacremonium recifei Species Nectriaceae 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 NPC94721 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 NPC94721 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