Natural Product: NPC266298

Natural Product IDNPC266298
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Cembrene-C
IUPAC Name (1E,3E,7E,11E)-1,7,11-trimethyl-4-propan-2-ylcyclotetradeca-1,3,7,11-tetraene
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2414202
PubChem CID 6521442
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0000008] Cembrane diterpenoids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey UJUWZMUCEGGBOH-YBJPMODXSA-N
Standard InCHI InChI=1S/C20H32/c1-16(2)20-14-12-18(4)10-6-8-17(3)9-7-11-19(5)13-15-20/h8,11-12,14,16H,6-7,9-10,13,15H2,1-5H3/b17-8+,18-12+,19-11+,20-14+
SMILES C/C/1=CCC/C(=C/CC/C(=C/C=C(CC1)/C(C)C)/C)/C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   272.25 Volume:   335.374
?
Van der Waals volume.
Dense:   0.812 LogP:   5.321
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.697
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.324
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   14.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.462 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.603 Fsp3:   0.6
MCE-18:   11.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.773 Fluc inhibitor:   0.137
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.004
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.99 Promiscuous compounds:   0.008

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.625 MDCK Permeability:   -4.793
Pgp-inhibitor:   1.0 Pgp-substrate:   0.002
PAMPA:   0.0
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.001
20% Bioavailability (F20%):   0.055 30% Bioavailability (F30%):   0.184
50% Bioavailability (F50%):   0.607

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.989
Plasma Protein Binding (PPB):   96.216% Volume Distribution (VD):   0.195
Fu: 3.826%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.007
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.871 CYP1A2-substrate:   0.88
CYP2C19-inhibitor:   0.984 CYP2C19-substrate:   0.075
CYP2C9-inhibitor:   0.618 CYP2C9-substrate:   0.095
CYP2D6-inhibitor:   0.913 CYP2D6-substrate:   0.427
CYP3A4-inhibitor:   0.039 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.009 CYP2C8-inhibitor:   0.999
HLM stability:   0.818
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  10.319 Half-life (T1/2):  0.438

ADMET: Toxicity

hERG Blockers:  0.056 hERG Blockers (10um):  0.072
Human Hepatotoxicity (H-HT):  0.737 Drug-induced Liver Injury (DILI):  0.845
AMES Toxicity:  0.036 Rat Oral Acute Toxicity:  0.015
Maximum Recommended Daily Dose:  0.529 Skin Sensitization:  0.88
Carcinogencity:  0.087 Eye Corrosion:  0.36
Eye Irritation:  0.997 Respiratory Toxicity:  0.233
Drug-induced Neurotoxicity:  0.662 Ototoxicity:  0.064
Hematotoxicity:  0.083 Drug-induced Nephrotoxicity:  0.425
Genotoxicity:  0.086 RPMI-8226 Immunitoxicity:  0.124
A549 Cytotoxicity:  0.081 Hek293 Cytotoxicity:  0.29
BCF:   3.712
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   4.898
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.608
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.229
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[10923847]
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[23859780]
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20809 Sarcophyton trocheliophorum Species Alcyoniidae 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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT178 Individual protein Protein-tyrosine phosphatase 1B Homo sapiens IC50 = 26600.0 nM PMID[1710653]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT34 Cell line BV-2 Mus musculus Inhibition = 85.45 % PMID[33857736]
NPT34 Cell line BV-2 Mus musculus Activity = 100.2 % PMID[33857736]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC266298 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7333 Intermediate Similarity NPC188789
0.6522 Remote Similarity NPC239039
0.6471 Remote Similarity NPC155849
0.6471 Remote Similarity NPC329686
0.5526 Remote Similarity NPC142423
0.5526 Remote Similarity NPC308294
0.5526 Remote Similarity NPC604966
0.5357 Remote Similarity NPC305759
0.5294 Remote Similarity NPC609378

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC266298 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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