Structure

Physi-Chem Properties

Molecular Weight:  296.18
Volume:  336.488
LogP:  5.585
LogD:  3.816
LogS:  -4.542
# Rotatable Bonds:  4
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.666
Synthetic Accessibility Score:  3.427
Fsp3:  0.3
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  2
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.874
MDCK Permeability:  1.3628170563606545e-05
Pgp-inhibitor:  0.159
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.986
30% Bioavailability (F30%):  0.922

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.034
Plasma Protein Binding (PPB):  97.37918853759766%
Volume Distribution (VD):  1.941
Pgp-substrate:  2.67061448097229%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.783
CYP2C19-inhibitor:  0.399
CYP2C19-substrate:  0.17
CYP2C9-inhibitor:  0.381
CYP2C9-substrate:  0.767
CYP2D6-inhibitor:  0.728
CYP2D6-substrate:  0.744
CYP3A4-inhibitor:  0.093
CYP3A4-substrate:  0.163

ADMET: Excretion

Clearance (CL):  6.276
Half-life (T1/2):  0.538

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.037
Drug-inuced Liver Injury (DILI):  0.309
AMES Toxicity:  0.458
Rat Oral Acute Toxicity:  0.276
Maximum Recommended Daily Dose:  0.743
Skin Sensitization:  0.954
Carcinogencity:  0.722
Eye Corrosion:  0.032
Eye Irritation:  0.933
Respiratory Toxicity:  0.823

Download Data

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

  Natural Product: NPC64464

Natural Product ID:  NPC64464
Common Name*:   CAAYVGWMDZSZAD-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CAAYVGWMDZSZAD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C20H24O2/c1-12(2)7-6-8-16-14(5)9-10-15-11-17(13(3)4)19(21)20(22)18(15)16/h9-11,13H,1,6-8H2,2-5H3
SMILES:  C=C(C)CCCc1c(C)ccc2C=C(C(C)C)C(=O)C(=O)c12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   157301
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000023] Naphthalenes
        • [CHEMONTID:0000153] Naphthoquinones

*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
NPO2717 Vatica cinerea Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. PMID[12608862]
NPO16570 Didemnum obscurum Species Didemnidae Eukaryota n.a. Tiruchandur coast in the Gulf of Mannar, Tamilnadu, India 2002-FEB PMID[15270574]
NPO6706 Arthrobotrys oligospora Species Orbiliaceae Eukaryota n.a. n.a. n.a. PMID[21568306]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[22804108]
NPO1425 Salvia palaestina Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[6677714]
NPO5795 Koelpinia linearis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2052 Hedyotis acutangula Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2052 Hedyotis acutangula Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15519 Lysimachia candida Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5795 Koelpinia linearis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9258 Plantago cornuti Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4487 Fritillaria thunbergii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1425 Salvia palaestina Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6706 Arthrobotrys oligospora Species Orbiliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18607 Eria macrophylla Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16570 Didemnum obscurum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21044 Sphaerellopsis filum Species Leptosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18270 Betula divaricata Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9079 Tephrosia egregia Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14820 Petasites spurius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19313 Herniaria fontanesii Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6977 Triopha carpenteri Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2052 Hedyotis acutangula Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9258 Plantago cornuti Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5784 Walsura chrysogyne Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5442 Bryum weigelii Species Bryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5795 Koelpinia linearis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4873 Plectranthus sylvestris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15519 Lysimachia candida Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12898 Rhaphiolepis umbellata Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11435 Tulipa sylvestris Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4487 Fritillaria thunbergii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19247 Viburnum jucundum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27607 Saussurea candicans Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13852 Pachysandra terminalis Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2717 Vatica cinerea Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10233 Nicotiana trigonophylla Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22284 Acacia myrtifolia Species Fabaceae 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 NPC64464 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 NPC64464 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