Structure

Physi-Chem Properties

Molecular Weight:  178.14
Volume:  202.513
LogP:  2.579
LogD:  2.592
LogS:  -1.971
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.521
Synthetic Accessibility Score:  3.87
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.523
MDCK Permeability:  1.9260687622590922e-05
Pgp-inhibitor:  0.067
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.453
30% Bioavailability (F30%):  0.049

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.906
Plasma Protein Binding (PPB):  74.95067596435547%
Volume Distribution (VD):  0.791
Pgp-substrate:  20.496177673339844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.204
CYP1A2-substrate:  0.594
CYP2C19-inhibitor:  0.183
CYP2C19-substrate:  0.892
CYP2C9-inhibitor:  0.103
CYP2C9-substrate:  0.624
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.65
CYP3A4-inhibitor:  0.287
CYP3A4-substrate:  0.281

ADMET: Excretion

Clearance (CL):  11.468
Half-life (T1/2):  0.711

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.195
Drug-inuced Liver Injury (DILI):  0.079
AMES Toxicity:  0.051
Rat Oral Acute Toxicity:  0.09
Maximum Recommended Daily Dose:  0.155
Skin Sensitization:  0.144
Carcinogencity:  0.933
Eye Corrosion:  0.422
Eye Irritation:  0.896
Respiratory Toxicity:  0.891

Download Data

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

  Natural Product: NPC31110

Natural Product ID:  NPC31110
Common Name*:   RKKGFWOMSDLRQL-SKDRFNHKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RKKGFWOMSDLRQL-SKDRFNHKSA-N
Standard InCHI:  InChI=1S/C12H18O/c1-9-4-3-5-10-6-7-11(13)8-12(9,10)2/h5,9H,3-4,6-8H2,1-2H3/t9-,12+/m1/s1
SMILES:  C[C@@H]1CCC=C2CCC(=O)C[C@@]12C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   6428337
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones

*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
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[14510614]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. stem n.a. PMID[21443171]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24869 Nicotiana rustica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23737 Allium turcomanicum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24110 Lippia alba Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12731 Porodaedalea pini Species Hymenochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24684 Eremanthus crotonoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21741 Araucaria angustifolia Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2617 Dracocephalum multicaule Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14889 Vachellia farnesiana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23423 Phellopterus littoralis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24716 Pulvinula constellatio Species Pyronemataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24490 Cussonia bancoensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19677 Cephalaria transsylvanica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25027 Cynoglossum creticum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22021 Teucrium spinosum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21168 Erylus lendenfeldi Species Geodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23283 Triptilion benaventei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22352 Lysimachia heterogenea Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24869 Nicotiana rustica Species Solanaceae 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 NPC31110 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 NPC31110 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