Structure

Physi-Chem Properties

Molecular Weight:  314.12
Volume:  319.711
LogP:  3.922
LogD:  2.607
LogS:  -3.811
# Rotatable Bonds:  2
TPSA:  75.99
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.888
Synthetic Accessibility Score:  2.902
Fsp3:  0.278
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.811
MDCK Permeability:  1.3004846550757065e-05
Pgp-inhibitor:  0.061
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.08
Plasma Protein Binding (PPB):  99.08100891113281%
Volume Distribution (VD):  0.406
Pgp-substrate:  1.2250500917434692%

ADMET: Metabolism

CYP1A2-inhibitor:  0.402
CYP1A2-substrate:  0.943
CYP2C19-inhibitor:  0.886
CYP2C19-substrate:  0.7
CYP2C9-inhibitor:  0.909
CYP2C9-substrate:  0.903
CYP2D6-inhibitor:  0.534
CYP2D6-substrate:  0.681
CYP3A4-inhibitor:  0.436
CYP3A4-substrate:  0.366

ADMET: Excretion

Clearance (CL):  7.393
Half-life (T1/2):  0.217

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.645
Drug-inuced Liver Injury (DILI):  0.925
AMES Toxicity:  0.066
Rat Oral Acute Toxicity:  0.884
Maximum Recommended Daily Dose:  0.626
Skin Sensitization:  0.924
Carcinogencity:  0.514
Eye Corrosion:  0.003
Eye Irritation:  0.87
Respiratory Toxicity:  0.741

Download Data

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

  Natural Product: NPC305881

Natural Product ID:  NPC305881
Common Name*:   DZTRDRPCROOSOG-CQSZACIVSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DZTRDRPCROOSOG-CQSZACIVSA-N
Standard InCHI:  InChI=1S/C18H18O5/c1-9-16(20)10(2)18-15(17(9)21)13(19)8-14(23-18)11-4-6-12(22-3)7-5-11/h4-7,14,20-21H,8H2,1-3H3/t14-/m1/s1
SMILES:  Cc1c(c(C)c2c(C(=O)C[C@H](c3ccc(cc3)OC)O2)c1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   49770782
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002596] 4'-O-methylated flavonoids

*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
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. fruit n.a. DOI[10.1016/S0040-4020(01)89039-6]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[11032480]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. rhizome n.a. PMID[12951487]
NPO4703 Solanum hispidum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[15217270]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. whole plant n.a. PMID[16079517]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota root bark n.a. n.a. PMID[16562837]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. PMID[16870425]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. fruit n.a. PMID[21028890]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. PMID[24013342]
NPO14359 Pentarhizidium orientale Species Onocleaceae Eukaryota Rhizomes n.a. n.a. PMID[28984452]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[FooDB]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6671 Ulva conglobata Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14359 Pentarhizidium orientale Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31232 Matteuccia orientalis Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3789 Lyonia formosa Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6671 Ulva conglobata Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14359 Pentarhizidium orientale Species Onocleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO183 Rhododendron simsii Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2828 Blaps mucronata Species Tenebrionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5638 Garcinia livingstonei Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8186 Ocotea minarum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7705 Navanax inermis Species Aglajidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27945 Cancrinia discoidea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1896 Proteus penneri Species Morganellaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO2384 Ircinia ramosa Species Irciniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO46 Onosma hispida Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4703 Solanum hispidum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7925 Asparagus officinalis Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6938 Astragalus dissectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO536 Dryopteris crassirhizoma Species Dryopteridaceae 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 NPC305881 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 NPC305881 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