Structure

Physi-Chem Properties

Molecular Weight:  314.12
Volume:  325.631
LogP:  3.28
LogD:  2.639
LogS:  -4.373
# Rotatable Bonds:  6
TPSA:  73.58
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.473
Synthetic Accessibility Score:  3.71
Fsp3:  0.278
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.613
MDCK Permeability:  1.9359167708898894e-05
Pgp-inhibitor:  0.937
Pgp-substrate:  0.009
Human Intestinal Absorption (HIA):  0.036
20% Bioavailability (F20%):  0.72
30% Bioavailability (F30%):  0.927

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.009
Plasma Protein Binding (PPB):  91.70394134521484%
Volume Distribution (VD):  3.184
Pgp-substrate:  6.723087310791016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.924
CYP1A2-substrate:  0.109
CYP2C19-inhibitor:  0.892
CYP2C19-substrate:  0.129
CYP2C9-inhibitor:  0.771
CYP2C9-substrate:  0.228
CYP2D6-inhibitor:  0.072
CYP2D6-substrate:  0.132
CYP3A4-inhibitor:  0.097
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  6.419
Half-life (T1/2):  0.625

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.903
Drug-inuced Liver Injury (DILI):  0.345
AMES Toxicity:  0.308
Rat Oral Acute Toxicity:  0.87
Maximum Recommended Daily Dose:  0.941
Skin Sensitization:  0.738
Carcinogencity:  0.869
Eye Corrosion:  0.015
Eye Irritation:  0.147
Respiratory Toxicity:  0.978

Download Data

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

  Natural Product: NPC143515

Natural Product ID:  NPC143515
Common Name*:   KUMRDPIXRZXXRO-KRWDZBQOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KUMRDPIXRZXXRO-KRWDZBQOSA-N
Standard InCHI:  InChI=1S/C18H18O5/c1-11(2)4-7-17(23-12(3)19)13-8-18(22-10-13)15-9-14(20)5-6-16(15)21/h4-6,8-10,17H,7H2,1-3H3/t17-/m0/s1
SMILES:  CC(=CC[C@@H](c1cc(C2=CC(=O)C=CC2=O)oc1)OC(=O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   157628
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001534] Quinone and hydroquinone lipids
          • [CHEMONTID:0002802] Prenylquinones

*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
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota roots n.a. n.a. PMID[10217724]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. PMID[12398531]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO20181 Dracaena arborea Species Asparagaceae Eukaryota bark Yaound, village of Bangoua, near Bangangt 2007-APR PMID[20553003]
NPO5119.1 Pseudomonas chlororaphis subsp. aurantiaca Subspecies Pseudomonadaceae Bacteria n.a. n.a. n.a. PMID[31999458]
NPO19871 Rubus arcticus Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18713 Strychnos usambarensis Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19871 Rubus arcticus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5119.1 Pseudomonas chlororaphis subsp. aurantiaca Subspecies Pseudomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO14913 Robinia neomexicana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20181 Dracaena arborea Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18550 Teucrium gnaphalodes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19789 Umbilicaria polyphylla Species Umbilicariaceae 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 NPC143515 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 NPC143515 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