Structure

Physi-Chem Properties

Molecular Weight:  222.2
Volume:  251.117
LogP:  3.962
LogD:  3.992
LogS:  -4.371
# Rotatable Bonds:  0
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.664
Synthetic Accessibility Score:  5.25
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.603
MDCK Permeability:  1.9129451175103895e-05
Pgp-inhibitor:  0.016
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.302
30% Bioavailability (F30%):  0.376

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.23
Plasma Protein Binding (PPB):  95.10669708251953%
Volume Distribution (VD):  1.231
Pgp-substrate:  5.450721740722656%

ADMET: Metabolism

CYP1A2-inhibitor:  0.696
CYP1A2-substrate:  0.687
CYP2C19-inhibitor:  0.783
CYP2C19-substrate:  0.927
CYP2C9-inhibitor:  0.521
CYP2C9-substrate:  0.229
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.331
CYP3A4-inhibitor:  0.344
CYP3A4-substrate:  0.685

ADMET: Excretion

Clearance (CL):  9.668
Half-life (T1/2):  0.153

ADMET: Toxicity

hERG Blockers:  0.065
Human Hepatotoxicity (H-HT):  0.388
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.524
Maximum Recommended Daily Dose:  0.419
Skin Sensitization:  0.781
Carcinogencity:  0.606
Eye Corrosion:  0.925
Eye Irritation:  0.751
Respiratory Toxicity:  0.956

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Similar NPs/Drugs  

  Natural Product: NPC20306

Natural Product ID:  NPC20306
Common Name*:   GGHMUJBZYLPWFD-CUZKYEQNSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GGHMUJBZYLPWFD-CUZKYEQNSA-N
Standard InCHI:  InChI=1S/C15H26O/c1-10-5-8-15(16)13(2,3)11-6-7-14(15,4)12(10)9-11/h10-12,16H,5-9H2,1-4H3/t10-,11+,12-,14-,15+/m0/s1
SMILES:  C[C@H]1CC[C@]2(C(C)(C)[C@@H]3CC[C@@]2(C)[C@H]1C3)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10955174
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary 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
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. root n.a. DOI[10.1016/S0040-4039(97)10844-9]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. root n.a. DOI[10.1021/np50075a009]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota roots n.a. n.a. PMID[12398547]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. leaf n.a. PMID[12575075]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. stem n.a. PMID[12575075]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[15577255]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. root n.a. PMID[15763368]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. root n.a. PMID[17253088]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. root n.a. PMID[18164718]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[18404355]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[19245261]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20151678]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[22281186]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota roots n.a. n.a. PMID[22381047]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[22703163]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota Fruits n.a. n.a. PMID[24328283]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[24704554]
NPO41740 Pichia pastoris strain co-expressing HPO and CPR [n.a.] Strain Pichiaceae Eukaryota n.a. n.a. n.a. PMID[24747046]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25068786]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25844502]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[27588326]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[28485933]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30188125]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[30758201]
NPO41920 A new engineered strain of Yarrowia Lipolytica ATCC 201249 [n.a.] Strain Dipodascaceae Eukaryota n.a. n.a. n.a. PMID[31053076]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32935986]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. root n.a. PMID[547813]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23188 Folium perillae n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29459 Folium pogostemonis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12766 Oleum pogostemonis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12766 Oleum pogostemonis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO23188 Folium perillae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO29459 Folium pogostemonis n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6336 Asarum sieboldii Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae 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]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30339 Nardostachys chinensis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6336 Asarum sieboldii Species Aristolochiaceae 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]
NPO29463 Pogostemon cablin Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14108 Nardostachys jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24846 Astragalus membranaceus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18007 Agrimonia pilosa Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15715 Astragalus mongholicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23548 Leonurus heterophyllus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17333 Valeriana officinalis Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6336 Asarum sieboldii Species Aristolochiaceae 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
NPT71 Cell Line HEK293 Homo sapiens CC50 > 20000.0 nM PMID[500111]
NPT20 Organism Candida albicans Candida albicans MIC > 20000.0 nM PMID[500111]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC > 20000.0 nM PMID[500111]
NPT19 Organism Escherichia coli Escherichia coli MIC > 20000.0 nM PMID[500111]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC > 20000.0 nM PMID[500111]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 20000.0 nM PMID[500111]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii MIC > 20000.0 nM PMID[500111]
NPT2922 Organism Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus MIC > 20000.0 nM PMID[500111]
NPT20950 CELL-LINE Erythrocyte n.a. HC10 > 20.0 uM PMID[500111]

☑ 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 NPC20306 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 NPC20306 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