Structure

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Physi-Chem Properties

Molecular Weight:  468.4
Volume:  531.553
LogP:  7.822
LogD:  6.354
LogS:  -7.167
# Rotatable Bonds:  2
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.285
Synthetic Accessibility Score:  4.922
Fsp3:  0.906
Lipinski Rule-of-5:  Accepted
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:  -5.099
MDCK Permeability:  3.543455750332214e-05
Pgp-inhibitor:  0.521
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.868
30% Bioavailability (F30%):  0.762

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.011
Plasma Protein Binding (PPB):  94.2810287475586%
Volume Distribution (VD):  1.127
Pgp-substrate:  1.7067676782608032%

ADMET: Metabolism

CYP1A2-inhibitor:  0.048
CYP1A2-substrate:  0.309
CYP2C19-inhibitor:  0.107
CYP2C19-substrate:  0.966
CYP2C9-inhibitor:  0.128
CYP2C9-substrate:  0.211
CYP2D6-inhibitor:  0.088
CYP2D6-substrate:  0.38
CYP3A4-inhibitor:  0.736
CYP3A4-substrate:  0.721

ADMET: Excretion

Clearance (CL):  2.838
Half-life (T1/2):  0.109

ADMET: Toxicity

hERG Blockers:  0.168
Human Hepatotoxicity (H-HT):  0.075
Drug-inuced Liver Injury (DILI):  0.072
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.082
Maximum Recommended Daily Dose:  0.425
Skin Sensitization:  0.567
Carcinogencity:  0.006
Eye Corrosion:  0.987
Eye Irritation:  0.476
Respiratory Toxicity:  0.485

Download Data

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

  Natural Product: NPC214134

Natural Product ID:  NPC214134
Common Name*:   RIDJSNUZLSTKKB-DWTGHIQGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RIDJSNUZLSTKKB-DWTGHIQGSA-N
Standard InCHI:  InChI=1S/C32H52O2/c1-20-12-15-29(6)18-19-31(8)23(27(29)21(20)2)10-11-25-30(7)16-14-26(34-22(3)33)28(4,5)24(30)13-17-32(25,31)9/h12,15,20-21,23-27H,10-11,13-14,16-19H2,1-9H3/t20-,21-,23-,24+,25-,26+,27-,29-,30+,31-,32-/m1/s1
SMILES:  C[C@@H]1C=C[C@]2(C)CC[C@]3(C)[C@H](CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)OC(=O)C)[C@H]2[C@@H]1C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   101553159
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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 NPC214134 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 NPC214134 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