Structure

Physi-Chem Properties

Molecular Weight:  236.21
Volume:  274.333
LogP:  5.011
LogD:  4.444
LogS:  -4.713
# Rotatable Bonds:  2
TPSA:  9.23
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.644
Synthetic Accessibility Score:  4.2
Fsp3:  0.875
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.545
MDCK Permeability:  1.6550351574551314e-05
Pgp-inhibitor:  0.941
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.812
30% Bioavailability (F30%):  0.149

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.341
Plasma Protein Binding (PPB):  92.9578628540039%
Volume Distribution (VD):  2.191
Pgp-substrate:  3.504805326461792%

ADMET: Metabolism

CYP1A2-inhibitor:  0.376
CYP1A2-substrate:  0.759
CYP2C19-inhibitor:  0.189
CYP2C19-substrate:  0.922
CYP2C9-inhibitor:  0.194
CYP2C9-substrate:  0.441
CYP2D6-inhibitor:  0.021
CYP2D6-substrate:  0.861
CYP3A4-inhibitor:  0.421
CYP3A4-substrate:  0.414

ADMET: Excretion

Clearance (CL):  7.164
Half-life (T1/2):  0.208

ADMET: Toxicity

hERG Blockers:  0.234
Human Hepatotoxicity (H-HT):  0.238
Drug-inuced Liver Injury (DILI):  0.824
AMES Toxicity:  0.136
Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.948
Carcinogencity:  0.579
Eye Corrosion:  0.991
Eye Irritation:  0.983
Respiratory Toxicity:  0.562

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

  Natural Product: NPC213348

Natural Product ID:  NPC213348
Common Name*:   OFGCDEUJOOZBRL-XFIYOXNOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  OFGCDEUJOOZBRL-XFIYOXNOSA-N
Standard InCHI:  InChI=1S/C16H28O/c1-11(2)13-8-9-16(4,17-5)15-7-6-12(3)14(15)10-13/h12-15H,1,6-10H2,2-5H3/t12-,13+,14-,15-,16+/m0/s1
SMILES:  C=C(C)[C@@H]1CC[C@](C)([C@H]2CC[C@H](C)[C@@H]2C1)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10633596
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002874] Guaianes

*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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO24979 Tetracera boiviniana Species Dilleniaceae Eukaryota n.a. n.a. n.a. PMID[10654414]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24470 Solanum angustifolium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25498 Xanthoparmelia xanthosorediata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25556 Amanita porphyria Species Amanitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24271 Geranium stepporum Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23901 Alseodaphne andersonii Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23379 Comatula cratera Species Comatulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21726 Physcomitrella patens Species Funariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24979 Tetracera boiviniana Species Dilleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24971 Rhododendron championiae Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22146 Schizanthus integrifolius 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 NPC213348 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 NPC213348 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