Natural Product: NPC604966

Natural Product IDNPC604966
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DTXHLWUSJGTDSH-LWARWICDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL4553863
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 DTXHLWUSJGTDSH-LWARWICDSA-N
Standard InCHI InChI=1S/C20H32O/c1-15(2)18-11-9-16(3)7-6-8-17(4)10-12-19-20(5,21-19)14-13-18/h8-9,11,15,19H,6-7,10,12-14H2,1-5H3/b16-9+,17-8+,18-11+/t19-,20-/m0/s1
SMILES C/C1=CC=C(C(C)C)CC[C@]2(C)O[C@H]2CC/C(C)=C/CC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   288.25 Volume:   338.244
?
Van der Waals volume.
Dense:   0.852 LogP:   4.911
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.765
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.932
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   16.0
TPSA:   12.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.427 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.383 Fsp3:   0.7
MCE-18:   34.588
?
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:   0.542 Fluc inhibitor:   0.007
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.023
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.969 Promiscuous compounds:   0.342

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.505 MDCK Permeability:   -4.718
Pgp-inhibitor:   0.999 Pgp-substrate:   0.005
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):   0.0
20% Bioavailability (F20%):   0.319 30% Bioavailability (F30%):   0.34
50% Bioavailability (F50%):   0.905

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.987
Plasma Protein Binding (PPB):   96.669% Volume Distribution (VD):   0.231
Fu: 3.737%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.055
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.412 CYP1A2-substrate:   0.734
CYP2C19-inhibitor:   0.92 CYP2C19-substrate:   0.167
CYP2C9-inhibitor:   0.095 CYP2C9-substrate:   0.093
CYP2D6-inhibitor:   0.295 CYP2D6-substrate:   0.201
CYP3A4-inhibitor:   0.208 CYP3A4-substrate:   0.998
CYP2B6-substrate:   0.004 CYP2C8-inhibitor:   0.991
HLM stability:   0.905
?
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):  11.076 Half-life (T1/2):  0.572

ADMET: Toxicity

hERG Blockers:  0.097 hERG Blockers (10um):  0.186
Human Hepatotoxicity (H-HT):  0.794 Drug-induced Liver Injury (DILI):  0.735
AMES Toxicity:  0.097 Rat Oral Acute Toxicity:  0.055
Maximum Recommended Daily Dose:  0.681 Skin Sensitization:  0.937
Carcinogencity:  0.211 Eye Corrosion:  0.098
Eye Irritation:  0.981 Respiratory Toxicity:  0.351
Drug-induced Neurotoxicity:  0.546 Ototoxicity:  0.118
Hematotoxicity:  0.094 Drug-induced Nephrotoxicity:  0.271
Genotoxicity:  0.421 RPMI-8226 Immunitoxicity:  0.155
A549 Cytotoxicity:  0.121 Hek293 Cytotoxicity:  0.463
BCF:   3.435
?
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:   4.74
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.474
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.797
?
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
NPO44423 Sinularia grayi Genus Sinulariidae Eukaryota 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
NPT30114 Cell line Splenocyte Mus musculus IC50 = 14000.0 nM PMID[31253536]
NPT30114 Cell line Splenocyte Mus musculus IC50 = 39200.0 nM PMID[31253536]
NPT30114 Cell line Splenocyte Mus musculus Ratio CC50/IC50 = 3.5 n.a. PMID[31253536]
NPT30114 Cell line Splenocyte Mus musculus Ratio CC50/IC50 = 1.3 n.a. PMID[31253536]
NPT30114 Cell line Splenocyte Mus musculus CC50 = 49100.0 nM PMID[31253536]

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 NPC604966 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
0.7234 Intermediate Similarity NPC607772
0.6818 Remote Similarity NPC606645
0.6304 Remote Similarity NPC239373
0.6304 Remote Similarity NPC329989
0.6122 Remote Similarity NPC475310
0.5745 Remote Similarity NPC127824
0.5714 Remote Similarity NPC329656
0.56 Remote Similarity NPC609651
0.5526 Remote Similarity NPC266298
0.5417 Remote Similarity NPC56419
0.5294 Remote Similarity NPC605688
0.5192 Remote Similarity NPC170377
0.5098 Remote Similarity NPC485573
0.5098 Remote Similarity NPC607547

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC604966 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
0.5217 Remote Similarity NPD2685 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