Structure

Physi-Chem Properties

Molecular Weight:  286.07
Volume:  258.771
LogP:  -0.212
LogD:  -0.087
LogS:  -1.496
# Rotatable Bonds:  3
TPSA:  136.68
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.472
Synthetic Accessibility Score:  3.428
Fsp3:  0.417
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.177
MDCK Permeability:  1.9756047549890354e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.107
Human Intestinal Absorption (HIA):  0.3
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.192
Plasma Protein Binding (PPB):  38.498268127441406%
Volume Distribution (VD):  0.289
Pgp-substrate:  60.76399612426758%

ADMET: Metabolism

CYP1A2-inhibitor:  0.039
CYP1A2-substrate:  0.039
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.105
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  1.857
Half-life (T1/2):  0.923

ADMET: Toxicity

hERG Blockers:  0.118
Human Hepatotoxicity (H-HT):  0.173
Drug-inuced Liver Injury (DILI):  0.827
AMES Toxicity:  0.078
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.116
Carcinogencity:  0.041
Eye Corrosion:  0.004
Eye Irritation:  0.244
Respiratory Toxicity:  0.076

Download Data

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

  Natural Product: NPC43312

Natural Product ID:  NPC43312
Common Name*:   PKCGDMKATCKBQD-ZFNBHVESSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PKCGDMKATCKBQD-ZFNBHVESSA-N
Standard InCHI:  InChI=1S/C12H14O8/c13-6-2-1-5(11(17)18)3-8(6)20-12-10(16)9(15)7(14)4-19-12/h1-3,7,9-10,12-16H,4H2,(H,17,18)/t7-,9-,10+,12-/m0/s1
SMILES:  c1cc(c(cc1C(=O)O)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

*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
NPO14923 Mollinedia costaricensis Species Monimiaceae Eukaryota n.a. n.a. n.a. PMID[21401141]
NPO20393 Hypolepis punctata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20393 Hypolepis punctata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18206 Centaurea horrida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13728 Metanarthecium luteoviride Species Nartheciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21129 Asterias glacialis Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20393 Hypolepis punctata Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14923 Mollinedia costaricensis Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18276 Uvaria kirkii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15823 Maytenus buxifolia Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18958 Podolepis longipedata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19962 Laetiporus versisporus Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21513 Astilbe myriantha Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21399 Diaphus suborbitalis Species Myctophidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19643 Dendrodoris krebsii Species Dendrodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13071 Sindora wallichii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8768 Koompassia malaccensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19742 Pluchea lanceolata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8062 Phlomoides hamosa Species Lamiaceae 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 NPC43312 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 NPC43312 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