Structure

Physi-Chem Properties

Molecular Weight:  218.06
Volume:  218.338
LogP:  1.576
LogD:  1.503
LogS:  -2.862
# Rotatable Bonds:  2
TPSA:  56.51
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.417
Synthetic Accessibility Score:  2.182
Fsp3:  0.167
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:  -4.668
MDCK Permeability:  3.4068529203068465e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.954

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.346
Plasma Protein Binding (PPB):  85.97415924072266%
Volume Distribution (VD):  0.732
Pgp-substrate:  28.055604934692383%

ADMET: Metabolism

CYP1A2-inhibitor:  0.979
CYP1A2-substrate:  0.611
CYP2C19-inhibitor:  0.488
CYP2C19-substrate:  0.076
CYP2C9-inhibitor:  0.158
CYP2C9-substrate:  0.773
CYP2D6-inhibitor:  0.156
CYP2D6-substrate:  0.576
CYP3A4-inhibitor:  0.371
CYP3A4-substrate:  0.241

ADMET: Excretion

Clearance (CL):  7.15
Half-life (T1/2):  0.758

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.248
Drug-inuced Liver Injury (DILI):  0.906
AMES Toxicity:  0.315
Rat Oral Acute Toxicity:  0.078
Maximum Recommended Daily Dose:  0.068
Skin Sensitization:  0.661
Carcinogencity:  0.903
Eye Corrosion:  0.169
Eye Irritation:  0.381
Respiratory Toxicity:  0.111

Download Data

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

  Natural Product: NPC126245

Natural Product ID:  NPC126245
Common Name*:   CXGTZEJDCYHXKR-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  CXGTZEJDCYHXKR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H10O4/c1-7-10(15-8(2)13)5-3-9-4-6-11(14)16-12(7)9/h3-6H,1-2H3
SMILES:  Cc1c(ccc2ccc(=O)oc12)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives

*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
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[10092191]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[10724012]
NPO28843 Astragalus zahlbruckneri Species Fabaceae Eukaryota Roots n.a. n.a. PMID[11575952]
NPO24786 Eunicea pinta Species Plexauridae Eukaryota n.a. n.a. n.a. PMID[12350138]
NPO1145 Coussarea paniculata Species Rubiaceae Eukaryota twigs n.a. n.a. PMID[12662105]
NPO22193 Ophioglossum petiolatum Species Ophioglossaceae Eukaryota n.a. whole plant n.a. PMID[15787440]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[15787462]
NPO28797 Hypoxylon carneum Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[16933875]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[9066761]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[9249977]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. PMID[9510911]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25414 Solanum berthaultii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25414 Solanum berthaultii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25414 Solanum berthaultii Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13482 Nierembergia hippomanica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24984 Hydrocotyle leucocephala Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25033 Pyrola calliantha Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22193 Ophioglossum petiolatum Species Ophioglossaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25289 Lonchocarpus salvadorensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25563 Axinella cannabina Species Axinellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24637 Oyedaea verbesinoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23383 Nigritella suaveolens n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24203 Sphoeroides vermicularis Species Tetraodontidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24066 0cardia brasiliensis Species 0cardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO1145 Coussarea paniculata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28797 Hypoxylon carneum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28843 Astragalus zahlbruckneri Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25233 Crocodylus niloticus Species Crocodylidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7329 Ligularia pleurocaulis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24786 Eunicea pinta Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24554 Hymenocallis speciosa 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 NPC126245 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 NPC126245 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