Natural Product: NPC476602

Natural Product IDNPC476602
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3-[(E)-2-[(1S,4aR,5S,6S,8aS)-6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]ethenyl]oxolan-2-one
IUPAC Name 3-[(E)-2-[(1S,4aR,5S,6S,8aS)-6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]ethenyl]oxolan-2-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 24776431
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones
          • [CHEMONTID:0001538] Diterpene lactones

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 OIUNBCUWBQRQCS-ZSLQUHRFSA-N
Standard InCHI InChI=1S/C20H30O4/c1-13-4-7-16-19(2,10-8-17(22)20(16,3)12-21)15(13)6-5-14-9-11-24-18(14)23/h5-6,14-17,21-22H,1,4,7-12H2,2-3H3/b6-5+/t14?,15-,16+,17-,19+,20+/m0/s1
SMILES C[C@]12CC[C@@H]([C@]([C@@H]1CCC(=C)[C@@H]2/C=C/C3CCOC3=O)(C)CO)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   334.21 Volume:   356.058
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Van der Waals volume.
Dense:   0.939 LogP:   2.683
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.847
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.54
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The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   19.0
TPSA:   66.76
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Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.615 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.798 Fsp3:   0.75
MCE-18:   56.4
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.101 Fluc inhibitor:   0.009
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.016
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.521 Promiscuous compounds:   0.397

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.172 MDCK Permeability:   -4.894
Pgp-inhibitor:   0.14 Pgp-substrate:   0.024
PAMPA:   0.244
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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):   0.015
20% Bioavailability (F20%):   0.949 30% Bioavailability (F30%):   0.961
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.279 MRP1:   0.362
Plasma Protein Binding (PPB):   69.024% Volume Distribution (VD):   -0.406
Fu: 27.167%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.771
OATP1B3 inhibitor:   0.804 BCRP inhibitor:   0.284
BSEP inhibitor:   0.877

ADMET: Metabolism

CYP1A2-inhibitor:   0.055 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.958 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.633 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.011 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.573
CYP2B6-substrate:   0.539 CYP2C8-inhibitor:   0.888
HLM stability:   0.181
?
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):  5.601 Half-life (T1/2):  1.378

ADMET: Toxicity

hERG Blockers:  0.037 hERG Blockers (10um):  0.314
Human Hepatotoxicity (H-HT):  0.577 Drug-induced Liver Injury (DILI):  0.273
AMES Toxicity:  0.322 Rat Oral Acute Toxicity:  0.571
Maximum Recommended Daily Dose:  0.565 Skin Sensitization:  0.964
Carcinogencity:  0.884 Eye Corrosion:  0.024
Eye Irritation:  0.898 Respiratory Toxicity:  0.758
Drug-induced Neurotoxicity:  0.58 Ototoxicity:  0.455
Hematotoxicity:  0.293 Drug-induced Nephrotoxicity:  0.49
Genotoxicity:  0.705 RPMI-8226 Immunitoxicity:  0.087
A549 Cytotoxicity:  0.305 Hek293 Cytotoxicity:  0.4
BCF:   0.748
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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:   3.503
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.346
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.626
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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
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. PMID[14738384]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota fruiting bodies n.a. n.a. PMID[16643055]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. PMID[17559265]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. PMID[24387703]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30573 Antrodia camphorata Species Fomitopsidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]

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
NPT2 Others Unspecified n.a. Activity = 45.1 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 43.8 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 39.6 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 34.9 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 36.7 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 29.5 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 29.3 % PMID[16643055]
NPT2 Others Unspecified n.a. Activity = 26.3 % PMID[16643055]

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 NPC476602 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
0.6786 Remote Similarity NPC152778
0.6786 Remote Similarity NPC205034
0.6102 Remote Similarity NPC474440
0.6034 Remote Similarity NPC77001
0.6034 Remote Similarity NPC131813
0.6034 Remote Similarity NPC139692
0.6034 Remote Similarity NPC253618
0.6 Remote Similarity NPC72845
0.6 Remote Similarity NPC16967
0.5833 Remote Similarity NPC159763
0.5833 Remote Similarity NPC278386
0.5833 Remote Similarity NPC124512
0.5738 Remote Similarity NPC242848
0.5517 Remote Similarity NPC79945
0.5484 Remote Similarity NPC191521
0.5439 Remote Similarity NPC476949
0.5424 Remote Similarity NPC310479
0.5224 Remote Similarity NPC73911
0.5079 Remote Similarity NPC162615

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC476602 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
0.5833 Remote Similarity NPD4225 Phase 3

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