Structure

Physi-Chem Properties

Molecular Weight:  152.12
Volume:  176.477
LogP:  2.133
LogD:  2.019
LogS:  -2.007
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.571
Synthetic Accessibility Score:  3.828
Fsp3:  0.6
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:  -4.477
MDCK Permeability:  1.4366264622367453e-05
Pgp-inhibitor:  0.005
Pgp-substrate:  0.041
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.926
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.901
Plasma Protein Binding (PPB):  48.966773986816406%
Volume Distribution (VD):  1.494
Pgp-substrate:  58.74668502807617%

ADMET: Metabolism

CYP1A2-inhibitor:  0.097
CYP1A2-substrate:  0.241
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.471
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.484
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.765
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.261

ADMET: Excretion

Clearance (CL):  8.62
Half-life (T1/2):  0.451

ADMET: Toxicity

hERG Blockers:  0.042
Human Hepatotoxicity (H-HT):  0.58
Drug-inuced Liver Injury (DILI):  0.093
AMES Toxicity:  0.096
Rat Oral Acute Toxicity:  0.187
Maximum Recommended Daily Dose:  0.972
Skin Sensitization:  0.237
Carcinogencity:  0.887
Eye Corrosion:  0.813
Eye Irritation:  0.984
Respiratory Toxicity:  0.861

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC201704

Natural Product ID:  NPC201704
Common Name*:   PNVTXOFNJFHXOK-VHSXEESVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PNVTXOFNJFHXOK-VHSXEESVSA-N
Standard InCHI:  InChI=1S/C10H16O/c1-7(2)9-5-4-8(3)10(11)6-9/h9-11H,1,3-6H2,2H3/t9-,10+/m0/s1
SMILES:  C=C(C)[C@H]1CCC(=C)[C@@H](C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6429040
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001401] Menthane monoterpenoids

*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
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[11975490]
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. PMID[15665489]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. Indonesian n.a. PMID[17311456]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. PMID[18679750]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota roots and rhizomes n.a. n.a. PMID[21570846]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[27128895]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[28841316]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota Resinous Wood n.a. n.a. PMID[29227647]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30129 Chenopodium ambrosioides Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15616 Solanum toxicarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14661 Blepharis sindica Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9283 Trichia favoginea Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8834 Cellulomonas biazotea Species Cellulomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11880 Latua pubiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15240 Saracha viscosa Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO890 Remijia pedunculata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3200 Arthrophytum leptocladum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO238 Lobelia st Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6239 Corbicula fluminea Species Corbiculidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14558 Aquilaria sinensis Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15150 Phebalium gracile Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14271 Spongia australis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14035 Cladosporium tenuissimum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11098 Stelletta inconspicua Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14156 Fragaria indica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12622 Rudbeckia hirta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13289 Frullania brittoniae Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27957.1 Pinus densiflora var. densiflora Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25443 Citrus reticulata Species Rutaceae 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 NPC201704 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 NPC201704 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