Structure

Physi-Chem Properties

Molecular Weight:  302.08
Volume:  299.829
LogP:  3.406
LogD:  2.037
LogS:  -4.194
# Rotatable Bonds:  3
TPSA:  115.06
# H-Bond Aceptor:  6
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.511
Synthetic Accessibility Score:  2.571
Fsp3:  0.125
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:  -5.115
MDCK Permeability:  9.267840141546912e-06
Pgp-inhibitor:  0.014
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.1
20% Bioavailability (F20%):  0.122
30% Bioavailability (F30%):  0.916

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  99.11420440673828%
Volume Distribution (VD):  0.493
Pgp-substrate:  1.51209557056427%

ADMET: Metabolism

CYP1A2-inhibitor:  0.875
CYP1A2-substrate:  0.145
CYP2C19-inhibitor:  0.203
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.623
CYP2C9-substrate:  0.714
CYP2D6-inhibitor:  0.467
CYP2D6-substrate:  0.313
CYP3A4-inhibitor:  0.307
CYP3A4-substrate:  0.154

ADMET: Excretion

Clearance (CL):  3.786
Half-life (T1/2):  0.56

ADMET: Toxicity

hERG Blockers:  0.063
Human Hepatotoxicity (H-HT):  0.084
Drug-inuced Liver Injury (DILI):  0.971
AMES Toxicity:  0.836
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.049
Skin Sensitization:  0.232
Carcinogencity:  0.153
Eye Corrosion:  0.006
Eye Irritation:  0.944
Respiratory Toxicity:  0.144

Download Data

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

  Natural Product: NPC85423

Natural Product ID:  NPC85423
Common Name*:   DYQDHRLBSZIKEM-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DYQDHRLBSZIKEM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C16H14O6/c1-7(17)9-3-4-12(21)15(16(9)22)14-11(20)6-5-10(19)13(14)8(2)18/h3-6,19-22H,1-2H3
SMILES:  CC(=O)c1ccc(c(c2c(ccc(c2C(=O)C)O)O)c1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10063465
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0000325] Biphenols

*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
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)80275-7]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[10217732]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16644212]
NPO280 Dysidea chlorea Species Dysideidae Eukaryota n.a. Okinawan n.a. PMID[16872148]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota Roots n.a. n.a. PMID[24054487]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota n.a. leaf n.a. PMID[24354204]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota n.a. twig n.a. PMID[24354204]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24412339]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota Latex n.a. n.a. PMID[26561866]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26716755]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5745 Randia formosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8942 Hedysarum coronarium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5745 Randia formosa Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3834 Periplaneta americana Species Blattoidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5486 Helicoon richonis Species Orbiliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1017 Dendrobium gibsonii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO280 Dysidea chlorea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6312 Picea engelmannii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8276 Harpullia ramiflora Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8809 Cynanchum wilfordii Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8680 Polypodium niponicum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4983 Bromelia pinguin Species Bromeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13333 Paenibacillus thiaminolyticus Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO28100 Jacobaea othonnae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2641 Marsupella aquatica Species Gymnomitriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8531 Centaurea ferox Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6086 Axinella polypoides Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO55 Croton urucurana Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12693 Mesembryanthemum tortuosum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8407 Polyporus fomentarius Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4010 Flemingia philippinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO626 Indigofera tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7220 Artemisia latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23643 Thalictrum aquilegiifolium Species Ranunculaceae 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 NPC85423 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 NPC85423 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