Structure

Physi-Chem Properties

Molecular Weight:  152.12
Volume:  170.557
LogP:  2.326
LogD:  2.742
LogS:  -2.168
# Rotatable Bonds:  1
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.563
Synthetic Accessibility Score:  3.971
Fsp3:  0.9
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:  -4.44
MDCK Permeability:  3.212707815691829e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.025
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.583
30% Bioavailability (F30%):  0.433

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.821
Plasma Protein Binding (PPB):  59.71393966674805%
Volume Distribution (VD):  0.89
Pgp-substrate:  44.2618293762207%

ADMET: Metabolism

CYP1A2-inhibitor:  0.351
CYP1A2-substrate:  0.516
CYP2C19-inhibitor:  0.154
CYP2C19-substrate:  0.913
CYP2C9-inhibitor:  0.073
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.113
CYP3A4-inhibitor:  0.271
CYP3A4-substrate:  0.634

ADMET: Excretion

Clearance (CL):  17.909
Half-life (T1/2):  0.457

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.411
Drug-inuced Liver Injury (DILI):  0.186
AMES Toxicity:  0.038
Rat Oral Acute Toxicity:  0.921
Maximum Recommended Daily Dose:  0.065
Skin Sensitization:  0.572
Carcinogencity:  0.86
Eye Corrosion:  0.971
Eye Irritation:  0.968
Respiratory Toxicity:  0.973

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

  Natural Product: NPC212950

Natural Product ID:  NPC212950
Common Name*:   NZDAOKCUPPNUTK-NRPADANISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NZDAOKCUPPNUTK-NRPADANISA-N
Standard InCHI:  InChI=1S/C10H16O/c1-6(2)7-4-9(11)10(3)5-8(7)10/h6-8H,4-5H2,1-3H3/t7-,8-,10-/m0/s1
SMILES:  CC(C)[C@@H]1CC(=O)[C@@]2(C)C[C@@H]12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   130914701
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
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. PMID[15665489]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. Indonesian n.a. PMID[17311456]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota roots and rhizomes n.a. n.a. PMID[21570846]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[28841316]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8834 Cellulomonas biazotea Species Cellulomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11880 Latua pubiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12622 Rudbeckia hirta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15240 Saracha viscosa Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13289 Frullania brittoniae Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3200 Arthrophytum leptocladum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6239 Corbicula fluminea Species Corbiculidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14271 Spongia australis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11098 Stelletta inconspicua Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27957.1 Pinus densiflora var. densiflora Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15150 Phebalium gracile Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14661 Blepharis sindica Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14035 Cladosporium tenuissimum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9283 Trichia favoginea Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14156 Fragaria indica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO890 Remijia pedunculata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15616 Solanum toxicarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO238 Lobelia st Species Campanulaceae 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 NPC212950 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 NPC212950 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