Natural Product: NPC603092

Natural Product IDNPC603092
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HWIKMSXIILZULT-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL465077
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 HWIKMSXIILZULT-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H28O/c1-2-3-4-5-6-7-8-9-10-12-16-13-11-14-17(18)15-16/h11,13-15,18H,2-10,12H2,1H3
SMILES CCCCCCCCCCCc1cccc(O)c1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   248.21 Volume:   294.913
?
Van der Waals volume.
Dense:   0.842 LogP:   6.777
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.256
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.478
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   6.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.545 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.709 Fsp3:   0.647
MCE-18:   5.0
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.547 Fluc inhibitor:   0.206
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.034
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.982 Promiscuous compounds:   0.164

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.058 MDCK Permeability:   -4.803
Pgp-inhibitor:   0.16 Pgp-substrate:   0.064
PAMPA:   0.007
?
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):   0.345
20% Bioavailability (F20%):   0.918 30% Bioavailability (F30%):   0.983
50% Bioavailability (F50%):   0.965

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.12 MRP1:   0.601
Plasma Protein Binding (PPB):   99.424% Volume Distribution (VD):   1.209
Fu: 1.102%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.837
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.804
BSEP inhibitor:   0.904

ADMET: Metabolism

CYP1A2-inhibitor:   0.022 CYP1A2-substrate:   0.986
CYP2C19-inhibitor:   0.36 CYP2C19-substrate:   0.587
CYP2C9-inhibitor:   0.996 CYP2C9-substrate:   0.873
CYP2D6-inhibitor:   0.992 CYP2D6-substrate:   0.507
CYP3A4-inhibitor:   0.005 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.998 CYP2C8-inhibitor:   0.999
HLM stability:   0.519
?
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):  5.209 Half-life (T1/2):  0.355

ADMET: Toxicity

hERG Blockers:  0.596 hERG Blockers (10um):  0.877
Human Hepatotoxicity (H-HT):  0.483 Drug-induced Liver Injury (DILI):  0.126
AMES Toxicity:  0.145 Rat Oral Acute Toxicity:  0.236
Maximum Recommended Daily Dose:  0.336 Skin Sensitization:  0.95
Carcinogencity:  0.255 Eye Corrosion:  0.954
Eye Irritation:  0.996 Respiratory Toxicity:  0.874
Drug-induced Neurotoxicity:  0.189 Ototoxicity:  0.18
Hematotoxicity:  0.147 Drug-induced Nephrotoxicity:  0.212
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.75 Hek293 Cytotoxicity:  0.481
BCF:   1.796
?
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:   5.391
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.958
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.106
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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
NPO4345 Caulocystis cephalornithos Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4345 Caulocystis cephalornithos Species Sargassaceae 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
NPT593 Organism Bursaphelenchus xylophilus Bursaphelenchus xylophilus MED = 5.0 ug PMID[18793855]
NPT28438 Unchecked Unchecked n.a. Selectivity Index = 0.2 n.a. PMID[18793855]
NPT28438 Unchecked Unchecked n.a. Selectivity Index = 7.06 n.a. PMID[18793855]

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
- Artemia salina LC50 = 1.0 ppm PMID[18793855]
- Artemia salina LC100 = 1.3 ppm PMID[18793855]
- Oryzias latipes LC50 = 3.8 ppm PMID[18793855]
- Oryzias latipes LC100 = 5.0 ppm PMID[18793855]

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 NPC603092 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 NPC3358
1.0 High Similarity NPC306884
0.8333 Intermediate Similarity NPC94139
0.8333 Intermediate Similarity NPC147284
0.8182 Intermediate Similarity NPC76938
0.8182 Intermediate Similarity NPC32714
0.8065 Intermediate Similarity NPC610566
0.8056 Intermediate Similarity NPC483454
0.8056 Intermediate Similarity NPC162314
0.7297 Intermediate Similarity NPC487734
0.725 Intermediate Similarity NPC210497
0.6875 Remote Similarity NPC606762
0.6765 Remote Similarity NPC294186
0.6765 Remote Similarity NPC147310
0.6765 Remote Similarity NPC137415
0.6765 Remote Similarity NPC166313
0.6765 Remote Similarity NPC123273
0.6765 Remote Similarity NPC192032
0.6765 Remote Similarity NPC318325
0.6765 Remote Similarity NPC24407
0.6765 Remote Similarity NPC11280
0.6429 Remote Similarity NPC192
0.6429 Remote Similarity NPC294741
0.625 Remote Similarity NPC487735
0.6216 Remote Similarity NPC241891
0.6216 Remote Similarity NPC134829
0.6129 Remote Similarity NPC27974
0.6061 Remote Similarity NPC210849
0.5882 Remote Similarity NPC246056
0.575 Remote Similarity NPC146798
0.575 Remote Similarity NPC222522
0.575 Remote Similarity NPC106396
0.575 Remote Similarity NPC94351
0.575 Remote Similarity NPC168303
0.5714 Remote Similarity NPC242240
0.5676 Remote Similarity NPC59506
0.561 Remote Similarity NPC487736
0.561 Remote Similarity NPC486908
0.5526 Remote Similarity NPC488411
0.5526 Remote Similarity NPC488410
0.5526 Remote Similarity NPC488409
0.55 Remote Similarity NPC53051
0.55 Remote Similarity NPC24404
0.55 Remote Similarity NPC313030
0.5455 Remote Similarity NPC599916
0.5349 Remote Similarity NPC71002
0.5349 Remote Similarity NPC249828
0.5263 Remote Similarity NPC37802
0.525 Remote Similarity NPC603218
0.5238 Remote Similarity NPC196479
0.5227 Remote Similarity NPC252105
0.5143 Remote Similarity NPC23167
0.5122 Remote Similarity NPC474839
0.5106 Remote Similarity NPC259942
0.5106 Remote Similarity NPC92624

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC603092 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
0.5526 Remote Similarity NPD846 Phase 4

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