Structure

Physi-Chem Properties

Molecular Weight:  198.16
Volume:  228.416
LogP:  4.351
LogD:  2.362
LogS:  -3.401
# Rotatable Bonds:  10
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.428
Synthetic Accessibility Score:  1.906
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.076
MDCK Permeability:  3.065522832912393e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.742
30% Bioavailability (F30%):  0.519

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.343
Plasma Protein Binding (PPB):  96.14147186279297%
Volume Distribution (VD):  0.277
Pgp-substrate:  2.178440570831299%

ADMET: Metabolism

CYP1A2-inhibitor:  0.084
CYP1A2-substrate:  0.272
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.335
CYP2C9-inhibitor:  0.125
CYP2C9-substrate:  0.979
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.29
CYP3A4-inhibitor:  0.032
CYP3A4-substrate:  0.038

ADMET: Excretion

Clearance (CL):  2.251
Half-life (T1/2):  0.787

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.061
Drug-inuced Liver Injury (DILI):  0.016
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.107
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.924
Carcinogencity:  0.133
Eye Corrosion:  0.982
Eye Irritation:  0.988
Respiratory Toxicity:  0.797

Download Data

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

  Natural Product: NPC116610

Natural Product ID:  NPC116610
Common Name*:   GZZPOFFXKUVNSW-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GZZPOFFXKUVNSW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H22O2/c1-2-3-4-5-6-7-8-9-10-11-12(13)14/h2H,1,3-11H2,(H,13,14)
SMILES:  C=CCCCCCCCCCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   125207
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-chain fatty acids

*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
NPO5716 Mallotus nudiflorus Species Euphorbiaceae Eukaryota n.a. bark n.a. DOI[10.1002/hlca.200590219]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. sclerotium n.a. PMID[21250700]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. PMID[24937646]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO24974 Zingiber montanum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7397 Tephrosia obovata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24974 Zingiber montanum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10253 Pithecellobium dulce Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9982 Heptacyclum zenkeri n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8629 Ruppia maritima Species Cymodoceaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9582 Ormocarpum kirkii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5716 Mallotus nudiflorus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9335 Gomophia watsoni n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5840 Stellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7196 Jaborosa parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2858 Ercolania funerea Species Limapontiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3823 Helichrysum stirlingii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1277 Pamburus missionis Species Rutaceae 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 NPC116610 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 NPC116610 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