Natural Product: NPC471274

Natural Product IDNPC471274
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XSEMXLZWKDTMJS-MDZDMXLPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 71745536
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols

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 XSEMXLZWKDTMJS-MDZDMXLPSA-N
Standard InCHI InChI=1S/C11H18O/c1-3-5-6-7-8-9-10-11(12)4-2/h2,9-12H,3,5-8H2,1H3/b10-9+
SMILES CCCCCCC=CC(C#C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   166.14 Volume:   199.693
?
Van der Waals volume.
Dense:   0.832 LogP:   3.262
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.798
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.747
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The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   2.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.365 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.212 Fsp3:   0.636
MCE-18:   1.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.006 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.006
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.997 Promiscuous compounds:   0.029

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.738 MDCK Permeability:   -4.694
Pgp-inhibitor:   0.001 Pgp-substrate:   0.001
PAMPA:   0.193
?
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):   0.035
20% Bioavailability (F20%):   0.009 30% Bioavailability (F30%):   0.05
50% Bioavailability (F50%):   0.302

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.703 MRP1:   0.001
Plasma Protein Binding (PPB):   98.512% Volume Distribution (VD):   0.209
Fu: 1.194%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.152
OATP1B3 inhibitor:   0.963 BCRP inhibitor:   0.695
BSEP inhibitor:   0.686

ADMET: Metabolism

CYP1A2-inhibitor:   0.003 CYP1A2-substrate:   0.974
CYP2C19-inhibitor:   0.967 CYP2C19-substrate:   0.102
CYP2C9-inhibitor:   0.997 CYP2C9-substrate:   0.815
CYP2D6-inhibitor:   0.078 CYP2D6-substrate:   0.858
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.026 CYP2C8-inhibitor:   0.997
HLM stability:   0.692
?
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):  5.838 Half-life (T1/2):  1.122

ADMET: Toxicity

hERG Blockers:  0.059 hERG Blockers (10um):  0.663
Human Hepatotoxicity (H-HT):  0.513 Drug-induced Liver Injury (DILI):  0.015
AMES Toxicity:  0.294 Rat Oral Acute Toxicity:  0.59
Maximum Recommended Daily Dose:  0.397 Skin Sensitization:  0.645
Carcinogencity:  0.141 Eye Corrosion:  0.954
Eye Irritation:  0.99 Respiratory Toxicity:  0.999
Drug-induced Neurotoxicity:  0.156 Ototoxicity:  0.684
Hematotoxicity:  0.011 Drug-induced Nephrotoxicity:  0.691
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.11
A549 Cytotoxicity:  0.009 Hek293 Cytotoxicity:  0.059
BCF:   1.865
?
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:   4.526
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.026
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.541
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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
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. red sea n.a. PMID[12762806]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[18027906]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[22469701]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. collected by hand at a depth of 10 m off the shore of Iriomote Island, Okinawa Prefecture, Japan 2009-JUN PMID[23855338]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[24948562]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. PMID[27015002]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. New Guinea n.a. PMID[8158156]
NPO33070 Callyspongia sp. Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]

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 NPC471274 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 NPC249670
0.9583 High Similarity NPC474642
0.9583 High Similarity NPC473913
0.8696 High Similarity NPC125122
0.8696 High Similarity NPC471276
0.8696 High Similarity NPC471280
0.8696 High Similarity NPC471281
0.8333 Intermediate Similarity NPC170776
0.8333 Intermediate Similarity NPC9273
0.8333 Intermediate Similarity NPC165447
0.8333 Intermediate Similarity NPC471959
0.8333 Intermediate Similarity NPC199286
0.8333 Intermediate Similarity NPC489046
0.8333 Intermediate Similarity NPC76198
0.8333 Intermediate Similarity NPC610719
0.8 Intermediate Similarity NPC607242
0.7931 Intermediate Similarity NPC473865
0.75 Intermediate Similarity NPC474644
0.7333 Intermediate Similarity NPC474643
0.6452 Remote Similarity NPC91226
0.6452 Remote Similarity NPC243546
0.6452 Remote Similarity NPC31194
0.6452 Remote Similarity NPC248884
0.625 Remote Similarity NPC471239
0.625 Remote Similarity NPC161838
0.625 Remote Similarity NPC72699
0.625 Remote Similarity NPC55383
0.6061 Remote Similarity NPC471960
0.6061 Remote Similarity NPC477727
0.6 Remote Similarity NPC600749
0.6 Remote Similarity NPC601019
0.5714 Remote Similarity NPC484320
0.5676 Remote Similarity NPC471278
0.5676 Remote Similarity NPC470966
0.5556 Remote Similarity NPC197272
0.5526 Remote Similarity NPC477661
0.5526 Remote Similarity NPC603233
0.5526 Remote Similarity NPC607245
0.5405 Remote Similarity NPC89824
0.5405 Remote Similarity NPC475477
0.5405 Remote Similarity NPC256656
0.5405 Remote Similarity NPC294278
0.5405 Remote Similarity NPC85079
0.5405 Remote Similarity NPC151782
0.5405 Remote Similarity NPC477723
0.5385 Remote Similarity NPC470970
0.5152 Remote Similarity NPC55068
0.5152 Remote Similarity NPC124183
0.5152 Remote Similarity NPC482802
0.5143 Remote Similarity NPC153538
0.5143 Remote Similarity NPC93639
0.5128 Remote Similarity NPC48058
0.5128 Remote Similarity NPC470963
0.5122 Remote Similarity NPC470969

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471274 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
0.5152 Remote Similarity NPD3210 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