Structure

Physi-Chem Properties

Molecular Weight:  236.18
Volume:  263.191
LogP:  2.65
LogD:  2.96
LogS:  -3.197
# Rotatable Bonds:  3
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.752
Synthetic Accessibility Score:  4.161
Fsp3:  0.867
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:  -4.717
MDCK Permeability:  1.7765172742656432e-05
Pgp-inhibitor:  0.888
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.177
30% Bioavailability (F30%):  0.89

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.919
Plasma Protein Binding (PPB):  66.13634490966797%
Volume Distribution (VD):  0.634
Pgp-substrate:  35.0747184753418%

ADMET: Metabolism

CYP1A2-inhibitor:  0.065
CYP1A2-substrate:  0.646
CYP2C19-inhibitor:  0.312
CYP2C19-substrate:  0.917
CYP2C9-inhibitor:  0.306
CYP2C9-substrate:  0.754
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.859
CYP3A4-inhibitor:  0.067
CYP3A4-substrate:  0.268

ADMET: Excretion

Clearance (CL):  7.369
Half-life (T1/2):  0.603

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.21
Drug-inuced Liver Injury (DILI):  0.293
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.174
Maximum Recommended Daily Dose:  0.163
Skin Sensitization:  0.094
Carcinogencity:  0.114
Eye Corrosion:  0.77
Eye Irritation:  0.661
Respiratory Toxicity:  0.039

Download Data

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

  Natural Product: NPC4997

Natural Product ID:  NPC4997
Common Name*:   GTUMAHOVZNSHNI-NJZAAPMLSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  GTUMAHOVZNSHNI-NJZAAPMLSA-N
Standard InCHI:  InChI=1S/C15H24O2/c1-10(16)5-6-11-13-12(17)7-8-15(13,4)9-14(11,2)3/h11,13H,5-9H2,1-4H3/t11-,13+,15+/m0/s1
SMILES:  CC(=O)CC[C@H]1[C@@H]2C(=O)CC[C@]2(C)CC1(C)C
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:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] 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
NPO8246 Lantana involucrata Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[15217280]
NPO4890 Streptomyces rimosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[17631493]
NPO13607 Arenaria kansuensis Species Scolopacidae Eukaryota n.a. n.a. n.a. PMID[17655145]
NPO4890 Streptomyces rimosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[1833366]
NPO9032 Geotrichum candidum Species Dipodascaceae Eukaryota n.a. n.a. n.a. PMID[20488699]
NPO14190 Streptopelia orientalis Species Columbidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13305 Mammea africana Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14190 Streptopelia orientalis Species Columbidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13305 Mammea africana Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13607 Arenaria kansuensis Species Scolopacidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13607 Arenaria kansuensis Species Scolopacidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8655 Wendlandia tinctoria Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7350 Sitotroga cerealella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7119 Endospermum diadenum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13305 Mammea africana Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2510 Pteris argentea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5412 Tedania anhelans Species Tedaniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4890 Streptomyces rimosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6089 Metacalypogeia alternifolia Species Calypogeiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9032 Geotrichum candidum Species Dipodascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11341 Eucalyptus piperita Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13497 Senecio trichopterygius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8246 Lantana involucrata Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13201 Diphasiastrum tristachyum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14882 Collariella gracilis Species Chaetomiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14190 Streptopelia orientalis Species Columbidae 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 NPC4997 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 NPC4997 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