Natural Product: NPC575853

Natural Product IDNPC575853
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 tetradecane-5,8-diol
IUPAC Name tetradecane-5,8-diol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 MAYQEXDWUHVQPK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H30O2/c1-3-5-7-8-10-14(16)12-11-13(15)9-6-4-2/h13-16H,3-12H2,1-2H3
SMILES CCCCCCC(O)CCC(O)CCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   230.22 Volume:   268.281
?
Van der Waals volume.
Dense:   0.858 LogP:   3.676
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.929
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.321
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   0.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.532 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.854 Fsp3:   1.0
MCE-18:   2.0
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.044 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.995 Promiscuous compounds:   0.09

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.068 MDCK Permeability:   -4.794
Pgp-inhibitor:   0.001 Pgp-substrate:   0.884
PAMPA:   0.825
?
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):   0.278
20% Bioavailability (F20%):   0.373 30% Bioavailability (F30%):   0.987
50% Bioavailability (F50%):   0.956

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.094 MRP1:   0.565
Plasma Protein Binding (PPB):   90.391% Volume Distribution (VD):   0.424
Fu: 9.664%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.116
OATP1B3 inhibitor:   0.881 BCRP inhibitor:   0.632
BSEP inhibitor:   0.278

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.759
CYP2C19-inhibitor:   0.785 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.988 CYP2C9-substrate:   0.159
CYP2D6-inhibitor:   0.603 CYP2D6-substrate:   0.248
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.046
CYP2B6-substrate:   0.016 CYP2C8-inhibitor:   0.332
HLM stability:   0.014
?
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):  8.438 Half-life (T1/2):  0.584

ADMET: Toxicity

hERG Blockers:  0.359 hERG Blockers (10um):  0.759
Human Hepatotoxicity (H-HT):  0.487 Drug-induced Liver Injury (DILI):  0.024
AMES Toxicity:  0.037 Rat Oral Acute Toxicity:  0.019
Maximum Recommended Daily Dose:  0.282 Skin Sensitization:  0.955
Carcinogencity:  0.111 Eye Corrosion:  0.95
Eye Irritation:  0.99 Respiratory Toxicity:  0.918
Drug-induced Neurotoxicity:  0.029 Ototoxicity:  0.85
Hematotoxicity:  0.137 Drug-induced Nephrotoxicity:  0.7
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.036
A549 Cytotoxicity:  0.203 Hek293 Cytotoxicity:  0.087
BCF:   1.879
?
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:   4.393
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.107
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.788
?
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
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Seeds n.a. n.a. PMID[28134521]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32415726]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37667613]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37917799]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38005226]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38067590]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39588261]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9138 Syzygium cumini Species Myrtaceae 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

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 NPC575853 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
0.7368 Intermediate Similarity NPC66124
0.7059 Intermediate Similarity NPC608484
0.6842 Remote Similarity NPC122962
0.6818 Remote Similarity NPC474392
0.6316 Remote Similarity NPC319034
0.6316 Remote Similarity NPC1748
0.6316 Remote Similarity NPC159845
0.6316 Remote Similarity NPC72324
0.6316 Remote Similarity NPC97967
0.6316 Remote Similarity NPC193062
0.6087 Remote Similarity NPC474914
0.5882 Remote Similarity NPC325345
0.5833 Remote Similarity NPC479534
0.5789 Remote Similarity NPC110884
0.5769 Remote Similarity NPC469781
0.5556 Remote Similarity NPC560
0.5455 Remote Similarity NPC249801
0.5455 Remote Similarity NPC46248
0.5357 Remote Similarity NPC106872
0.5294 Remote Similarity NPC252154

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC575853 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
0.5882 Remote Similarity NPD8988 Clinical (unspecified phase)

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