Structure

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Physi-Chem Properties

Molecular Weight:  500.35
Volume:  532.071
LogP:  5.096
LogD:  4.242
LogS:  -5.072
# Rotatable Bonds:  3
TPSA:  68.29
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  6
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.515
Synthetic Accessibility Score:  5.35
Fsp3:  0.903
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.106
MDCK Permeability:  2.3879725631559268e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.773
30% Bioavailability (F30%):  0.823

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.011
Plasma Protein Binding (PPB):  90.29902648925781%
Volume Distribution (VD):  2.515
Pgp-substrate:  5.386312484741211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.663
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.876
CYP2C9-inhibitor:  0.111
CYP2C9-substrate:  0.022
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.093
CYP3A4-inhibitor:  0.663
CYP3A4-substrate:  0.761

ADMET: Excretion

Clearance (CL):  4.987
Half-life (T1/2):  0.12

ADMET: Toxicity

hERG Blockers:  0.176
Human Hepatotoxicity (H-HT):  0.325
Drug-inuced Liver Injury (DILI):  0.049
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.519
Maximum Recommended Daily Dose:  0.679
Skin Sensitization:  0.926
Carcinogencity:  0.024
Eye Corrosion:  0.109
Eye Irritation:  0.053
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC471627

Natural Product ID:  NPC471627
Common Name*:   12-Deacetyl-12-(2-Methylbutanoxyl)Turrapubin A
IUPAC Name:   (5R,7R,8S,9R,10R,13S,14R,17S)-17-[(2R,3S,5R)-5-[(2S)-3,3-dimethyloxiran-2-yl]-2-methoxyoxolan-3-yl]-7-hydroxy-4,4,8,10,13-pentamethyl-5,6,7,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-3-one
Synonyms:  
Standard InCHIKey:  PPZXDUFPMKSAJC-SQRKLTNRSA-N
Standard InCHI:  InChI=1S/C31H48O5/c1-27(2)22-16-24(33)31(7)20-10-9-18(17-15-19(35-26(17)34-8)25-28(3,4)36-25)29(20,5)13-11-21(31)30(22,6)14-12-23(27)32/h12,14,17-22,24-26,33H,9-11,13,15-16H2,1-8H3/t17-,18-,19+,20+,21+,22-,24+,25-,26+,29-,30+,31-/m0/s1
SMILES:  CO[C@@H]1O[C@H](C[C@H]1[C@@H]1CC[C@@H]2[C@@]1(C)CC[C@H]1[C@@]2(C)[C@H](O)C[C@@H]2[C@]1(C)C=CC(=O)C2(C)C)[C@@H]1OC1(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3038143
PubChem CID:   73357327
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids
          • [CHEMONTID:0002380] Limonoids

*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

☑ 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

☑ 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

☑ 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 NPC471627 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

  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 NPC471627 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

  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