Natural Product: NPC113639

Natural Product IDNPC113639
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
QPIUBKNTZMBLLI-ASFQSAAXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1689087
PubChem CID NA
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001760] Dolabellane and neodolabellane diterpenoids

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 QPIUBKNTZMBLLI-ASFQSAAXSA-N
Standard InCHI InChI=1S/C22H36O3/c1-15-8-7-9-16(2)14-19(25-17(3)23)20-18(21(4,5)24)11-13-22(20,6)12-10-15/h9-10,12,15,18-20,24H,7-8,11,13-14H2,1-6H3/b12-10+,16-9+/t15-,18-,19+,20-,22+/m1/s1
SMILES C[C@@H]1CC/C=C(C)/C[C@@H]([C@H]2[C@@H](CC[C@]2(C)/C=C/1)C(C)(C)O)OC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   348.27 Volume:   390.417
?
Van der Waals volume.
Dense:   0.892 LogP:   3.83
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.596
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.061
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   16.0
TPSA:   46.53
?
Topological Polar Surface Area.
H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.561 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.016 Fsp3:   0.773
MCE-18:   45.231
?
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.477 Fluc inhibitor:   0.203
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.691 Promiscuous compounds:   0.521

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.973 MDCK Permeability:   -4.847
Pgp-inhibitor:   0.996 Pgp-substrate:   0.018
PAMPA:   0.011
?
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%):   0.086 30% Bioavailability (F30%):   0.46
50% Bioavailability (F50%):   0.925

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.004 MRP1:   0.586
Plasma Protein Binding (PPB):   96.269% Volume Distribution (VD):   -0.228
Fu: 4.869%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.262
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.902 CYP1A2-substrate:   0.03
CYP2C19-inhibitor:   0.983 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.065 CYP2C9-substrate:   0.034
CYP2D6-inhibitor:   0.043 CYP2D6-substrate:   0.478
CYP3A4-inhibitor:   0.142 CYP3A4-substrate:   0.068
CYP2B6-substrate:   0.004 CYP2C8-inhibitor:   0.97
HLM stability:   0.916
?
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):  7.56 Half-life (T1/2):  0.353

ADMET: Toxicity

hERG Blockers:  0.017 hERG Blockers (10um):  0.025
Human Hepatotoxicity (H-HT):  0.685 Drug-induced Liver Injury (DILI):  0.328
AMES Toxicity:  0.297 Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.194 Skin Sensitization:  0.988
Carcinogencity:  0.633 Eye Corrosion:  0.179
Eye Irritation:  0.898 Respiratory Toxicity:  0.282
Drug-induced Neurotoxicity:  0.014 Ototoxicity:  0.367
Hematotoxicity:  0.441 Drug-induced Nephrotoxicity:  0.796
Genotoxicity:  0.132 RPMI-8226 Immunitoxicity:  0.063
A549 Cytotoxicity:  0.071 Hek293 Cytotoxicity:  0.232
BCF:   1.463
?
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:   3.921
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.553
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.904
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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
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota roots n.a. n.a. PMID[11325249]
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. at a depth of 0.1-1 m, Elafonissos Island (3630' N, 2258' E), south of Peloponnese, Greece 2004-APR PMID[21190330]
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. n.a. n.a. PMID[21190330]
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. Elafonissos Island (GPS coordinates 3630' N, 2258' E), south of Peloponnese, Greece 2004-APR PMID[21190330]
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16565 Lindera oldhami Species Tineidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21494 Eryngium maritimum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20488 Abies homolepis Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17330 Pseudopotamilla occelata Species Sabellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19911 Arachniodes festina Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27967 Betula glandulosa Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20420 Helenium brevifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20221 Maytenus truncata Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18865 Tetracentron sinense Species Trochodendraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20558 Pseudevernia ericetorum Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21169 Salvia blepharochlaena Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21306 Alpinia pinnanensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17838 Aster flaccidus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20838 Cleome pentaphylla Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16565 Lindera oldhami Species Tineidae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[21190330]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 64.0 ug.mL-1 PMID[21190330]

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 NPC113639 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
0.5472 Remote Similarity NPC323153

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC113639 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