Structure

Physi-Chem Properties

Molecular Weight:  270.05
Volume:  265.186
LogP:  3.069
LogD:  2.542
LogS:  -4.323
# Rotatable Bonds:  1
TPSA:  83.83
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.705
Synthetic Accessibility Score:  2.155
Fsp3:  0.067
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.801
MDCK Permeability:  1.709083517198451e-05
Pgp-inhibitor:  0.112
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.013
30% Bioavailability (F30%):  0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.11
Plasma Protein Binding (PPB):  99.44971466064453%
Volume Distribution (VD):  0.449
Pgp-substrate:  1.6108109951019287%

ADMET: Metabolism

CYP1A2-inhibitor:  0.932
CYP1A2-substrate:  0.692
CYP2C19-inhibitor:  0.195
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.605
CYP2C9-substrate:  0.66
CYP2D6-inhibitor:  0.359
CYP2D6-substrate:  0.287
CYP3A4-inhibitor:  0.772
CYP3A4-substrate:  0.177

ADMET: Excretion

Clearance (CL):  9.469
Half-life (T1/2):  0.445

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.051
Drug-inuced Liver Injury (DILI):  0.9
AMES Toxicity:  0.87
Rat Oral Acute Toxicity:  0.217
Maximum Recommended Daily Dose:  0.568
Skin Sensitization:  0.121
Carcinogencity:  0.924
Eye Corrosion:  0.004
Eye Irritation:  0.939
Respiratory Toxicity:  0.069

Download Data

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

  Natural Product: NPC224533

Natural Product ID:  NPC224533
Common Name*:   HULRBUQQNBFVIW-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HULRBUQQNBFVIW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C15H10O5/c1-20-11-5-4-9-12(15(11)19)14(18)8-3-2-7(16)6-10(8)13(9)17/h2-6,16,19H,1H3
SMILES:  COc1ccc2c(C(=O)c3ccc(cc3C2=O)O)c1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   132521
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes
        • [CHEMONTID:0000151] Anthraquinones
          • [CHEMONTID:0001598] Hydroxyanthraquinones

*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
NPO30972 Morinda officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13324 Euphorbia ingens Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27363 Gynochthodes officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30972 Morinda officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27363 Gynochthodes officinalis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15917 Monilinia fructigena Species Sclerotiniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26859 Solanum curtipes Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13324 Euphorbia ingens Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2868 Perna viridis Species Mytilidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO861 Siphonaria funiculata Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13446 Stachys recta Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11734 Chara corallina Species Characeae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27363 Gynochthodes officinalis Species Rubiaceae 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 NPC224533 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 NPC224533 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