Natural Product: NPC88359

Natural Product IDNPC88359
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ITYNGVSTWVVPIC-RGDJUOJXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 94249462
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0001781] Aromadendrane sesquiterpenoids
            • [CHEMONTID:0003562] 5,10-cycloaromadendrane sesquiterpenoids

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 ITYNGVSTWVVPIC-RGDJUOJXSA-N
Standard InCHI InChI=1S/C15H24/c1-9-6-8-12-14(15(12,3)4)13-10(2)5-7-11(9)13/h10-14H,1,5-8H2,2-4H3/t10-,11-,12+,13-,14+/m1/s1
SMILES C=C1CC[C@H]2[C@@H]([C@@H]3[C@H](C)CC[C@H]13)C2(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   204.19 Volume:   239.69
?
Van der Waals volume.
Dense:   0.852 LogP:   5.215
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.891
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.332
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   14.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.517 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.223 Fsp3:   0.867
MCE-18:   48.857
?
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:   0.377 Fluc inhibitor:   0.071
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.017
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.719 Promiscuous compounds:   0.133

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.8 MDCK Permeability:   -4.865
Pgp-inhibitor:   0.752 Pgp-substrate:   0.019
PAMPA:   0.003
?
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):   0.001
20% Bioavailability (F20%):   0.084 30% Bioavailability (F30%):   0.181
50% Bioavailability (F50%):   0.555

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.191 MRP1:   0.473
Plasma Protein Binding (PPB):   97.521% Volume Distribution (VD):   0.652
Fu: 3.317%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.938
OATP1B3 inhibitor:   0.806 BCRP inhibitor:   0.402
BSEP inhibitor:   0.933

ADMET: Metabolism

CYP1A2-inhibitor:   0.294 CYP1A2-substrate:   0.962
CYP2C19-inhibitor:   0.988 CYP2C19-substrate:   0.252
CYP2C9-inhibitor:   0.215 CYP2C9-substrate:   0.274
CYP2D6-inhibitor:   0.094 CYP2D6-substrate:   0.328
CYP3A4-inhibitor:   0.866 CYP3A4-substrate:   0.96
CYP2B6-substrate:   0.479 CYP2C8-inhibitor:   0.796
HLM stability:   0.944
?
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):  11.964 Half-life (T1/2):  1.521

ADMET: Toxicity

hERG Blockers:  0.079 hERG Blockers (10um):  0.427
Human Hepatotoxicity (H-HT):  0.534 Drug-induced Liver Injury (DILI):  0.336
AMES Toxicity:  0.445 Rat Oral Acute Toxicity:  0.305
Maximum Recommended Daily Dose:  0.349 Skin Sensitization:  0.407
Carcinogencity:  0.695 Eye Corrosion:  0.629
Eye Irritation:  0.979 Respiratory Toxicity:  0.696
Drug-induced Neurotoxicity:  0.468 Ototoxicity:  0.385
Hematotoxicity:  0.459 Drug-induced Nephrotoxicity:  0.219
Genotoxicity:  0.192 RPMI-8226 Immunitoxicity:  0.059
A549 Cytotoxicity:  0.274 Hek293 Cytotoxicity:  0.36
BCF:   3.019
?
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:   4.221
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.833
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.971
?
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
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. PMID[15665489]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. Indonesian n.a. PMID[17311456]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota roots and rhizomes n.a. n.a. PMID[21570846]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[28841316]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[32260539]
NPO1428 Linzia glabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3200 Arthrophytum leptocladum n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO14661 Blepharis sindica Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8834 Cellulomonas biazotea Species Cellulomonadaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO14035 Cladosporium tenuissimum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6239 Corbicula fluminea Species Corbiculidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14156 Fragaria indica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13289 Frullania brittoniae Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11880 Latua pubiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO238 Lobelia st Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15150 Phebalium gracile Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27957.1 Pinus densiflora var. densiflora Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO890 Remijia pedunculata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12622 Rudbeckia hirta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15240 Saracha viscosa Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15616 Solanum toxicarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14271 Spongia australis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11098 Stelletta inconspicua Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9283 Trichia favoginea Species Trichiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1988 Conocliniopsis prasiifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14752 Sinopodophyllum emodi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14035 Cladosporium tenuissimum Species Cladosporiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14156 Fragaria indica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5517 Rhododendron tomentosum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15616 Solanum toxicarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8834 Cellulomonas biazotea Species Cellulomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11880 Latua pubiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15240 Saracha viscosa Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3200 Arthrophytum leptocladum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3860 Allium victorialis Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6239 Corbicula fluminea Species Corbiculidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14271 Spongia australis Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11098 Stelletta inconspicua Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27957.1 Pinus densiflora var. densiflora Varieties Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1988 Conocliniopsis prasiifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1428 Linzia glabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14661 Blepharis sindica Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9283 Trichia favoginea Species Trichiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15432 Sarcodon aspratus Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO890 Remijia pedunculata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO238 Lobelia st Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4485 Lamellodysidea herbacea Species Dysideidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12622 Rudbeckia hirta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13289 Frullania brittoniae Species Frullaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15150 Phebalium gracile Species Rutaceae 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

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 NPC88359 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 NPC90803
1.0 High Similarity NPC23145
1.0 High Similarity NPC90506
0.5111 Remote Similarity NPC471662

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC88359 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