Structure

Physi-Chem Properties

Molecular Weight:  254.19
Volume:  268.698
LogP:  2.298
LogD:  2.764
LogS:  -2.403
# Rotatable Bonds:  2
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.698
Synthetic Accessibility Score:  4.68
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.798
MDCK Permeability:  0.0001078787972801365
Pgp-inhibitor:  0.0
Pgp-substrate:  0.401
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.87
Plasma Protein Binding (PPB):  78.19055938720703%
Volume Distribution (VD):  0.728
Pgp-substrate:  13.336193084716797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.216
CYP1A2-substrate:  0.611
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.816
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.132
CYP3A4-inhibitor:  0.208
CYP3A4-substrate:  0.274

ADMET: Excretion

Clearance (CL):  8.368
Half-life (T1/2):  0.734

ADMET: Toxicity

hERG Blockers:  0.085
Human Hepatotoxicity (H-HT):  0.279
Drug-inuced Liver Injury (DILI):  0.036
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.053
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.434
Carcinogencity:  0.372
Eye Corrosion:  0.823
Eye Irritation:  0.644
Respiratory Toxicity:  0.966

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

  Natural Product: NPC284265

Natural Product ID:  NPC284265
Common Name*:   XJCYHYLKHMEKAZ-CVEQBJKISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XJCYHYLKHMEKAZ-CVEQBJKISA-N
Standard InCHI:  InChI=1S/C15H26O3/c1-9-3-4-10-12(9)13-11(14(13,2)7-16)5-6-15(10,18)8-17/h9-13,16-18H,3-8H2,1-2H3/t9-,10+,11-,12-,13-,14-,15-/m1/s1
SMILES:  C[C@@H]1CC[C@H]2[C@@H]1[C@H]1[C@@H](CC[C@]2(CO)O)[C@@]1(C)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11076000
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0001781] Aromadendrane sesquiterpenoids
            • [CHEMONTID:0003562] 5,10-cycloaromadendrane 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
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[11575955]
NPO14137 Rhodomela confervoides Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[15217289]
NPO14137 Rhodomela confervoides Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[15921411]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[16268553]
NPO14137 Rhodomela confervoides Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[16499317]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. Fijian red alga n.a. PMID[16724831]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota stems Yunnan Province, China 2004 PMID[17253844]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[17715978]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems purchased from Kyoungdong Oriental Herbal Market, Seoul, Korea 2006-APR PMID[18052323]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. Fijian red alga n.a. PMID[20141173]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23022271]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota Stems n.a. n.a. PMID[27310249]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. PMID[30407005]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO60 Neoshirakia japonica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15280 Sideritis grandiflora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5019 Mespilus germanica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1575 Mikania luetzelburgii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6178 Solanum euacanthum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8966 Callophycus serratus Species Solieriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4048 Inga longispica Species Oecophoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13053 Corydalis conspersa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14137 Rhodomela confervoides Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3894 Dendrobium nobile Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO791 Laburnum anagyroides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO326 Pittosporum brevicalyx Species Pittosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15662 Ligustrum ovalifolium Species Oleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11242 Gynochthodes parvifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO60 Neoshirakia japonica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4581 Ungernia victoris Species Amaryllidaceae 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 NPC284265 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 NPC284265 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