Natural Product: NPC489304

Natural Product IDNPC489304
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 RLCBOPJHZRVMGC-VIRABCJISA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10829117
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002517] Chamigranes

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 RLCBOPJHZRVMGC-VIRABCJISA-N
Standard InCHI InChI=1S/C15H23BrO2/c1-10-9-11(17)12(16)13(2,3)15(10)7-5-14(4,18)6-8-15/h5,7,11-12,17-18H,1,6,8-9H2,2-4H3/t11-,12-,14+,15-/m0/s1
SMILES C=C1C[C@@H]([C@@H](C(C)(C)[C@@]21C=C[C@](C)(CC2)O)Br)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   314.09 Volume:   282.474
?
Van der Waals volume.
Dense:   1.112 LogP:   2.291
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.494
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.886
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   13.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.532 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.565 Fsp3:   0.733
MCE-18:   65.077
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.162 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.007
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.026
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.893 Promiscuous compounds:   0.203

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.148 MDCK Permeability:   -4.803
Pgp-inhibitor:   0.219 Pgp-substrate:   0.483
PAMPA:   0.941
?
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):   0.043
20% Bioavailability (F20%):   0.371 30% Bioavailability (F30%):   0.383
50% Bioavailability (F50%):   0.86

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.433 MRP1:   0.849
Plasma Protein Binding (PPB):   77.642% Volume Distribution (VD):   0.032
Fu: 12.973%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.859
OATP1B3 inhibitor:   0.716 BCRP inhibitor:   0.262
BSEP inhibitor:   0.894

ADMET: Metabolism

CYP1A2-inhibitor:   0.005 CYP1A2-substrate:   0.02
CYP2C19-inhibitor:   0.027 CYP2C19-substrate:   0.022
CYP2C9-inhibitor:   0.034 CYP2C9-substrate:   0.017
CYP2D6-inhibitor:   0.005 CYP2D6-substrate:   0.195
CYP3A4-inhibitor:   0.043 CYP3A4-substrate:   0.051
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.12
HLM stability:   0.322
?
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):  8.339 Half-life (T1/2):  1.559

ADMET: Toxicity

hERG Blockers:  0.028 hERG Blockers (10um):  0.209
Human Hepatotoxicity (H-HT):  0.537 Drug-induced Liver Injury (DILI):  0.393
AMES Toxicity:  0.604 Rat Oral Acute Toxicity:  0.526
Maximum Recommended Daily Dose:  0.617 Skin Sensitization:  0.965
Carcinogencity:  0.893 Eye Corrosion:  0.666
Eye Irritation:  0.994 Respiratory Toxicity:  0.725
Drug-induced Neurotoxicity:  0.635 Ototoxicity:  0.344
Hematotoxicity:  0.31 Drug-induced Nephrotoxicity:  0.736
Genotoxicity:  0.225 RPMI-8226 Immunitoxicity:  0.078
A549 Cytotoxicity:  0.24 Hek293 Cytotoxicity:  0.559
BCF:   0.418
?
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:   2.95
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.208
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.472
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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
NPO21610 Laurencia rigida Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[9358636]
NPO21610 Laurencia rigida Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21610 Laurencia rigida Species Rhodomelaceae 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

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1231 Organism Microbotryum violaceum Microbotryum violaceum IZ = 5.0 mm PMID[9358636]
NPT637 Organism Fusarium oxysporum Fusarium oxysporum IZ = 0.0 mm PMID[9358636]
NPT19 Organism Escherichia coli Escherichia coli IZ = 0.0 mm PMID[9358636]
NPT1234 Organism Chlorella fusca Chlorella fusca IZ = 0.0 mm PMID[9358636]
NPT1233 Organism Mycotypha microspora Mycotypha microspora IZ = 4.0 mm PMID[9358636]
NPT1232 Organism Eurotium repens Eurotium repens IZ = 0.0 mm PMID[9358636]
NPT1230 Organism Bacillus megaterium Bacillus megaterium IZ = 0.0 mm PMID[9358636]

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 NPC489304 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
1.0 High Similarity NPC113024
0.8108 Intermediate Similarity NPC483533
0.8108 Intermediate Similarity NPC483532
0.8108 Intermediate Similarity NPC311891
0.7179 Intermediate Similarity NPC215307
0.7179 Intermediate Similarity NPC274750
0.6585 Remote Similarity NPC109900
0.6 Remote Similarity NPC483535
0.5116 Remote Similarity NPC474946
0.5116 Remote Similarity NPC35397

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC489304 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