Natural Product: NPC256024

Natural Product IDNPC256024
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MHUYBIUXLMLCJM-BREBYQMCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101609001
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols

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 MHUYBIUXLMLCJM-BREBYQMCSA-N
Standard InCHI InChI=1S/C13H20O/c1-9-10(14)8-11-12(2,3)6-5-7-13(9,11)4/h5,7-10,14H,6H2,1-4H3/t9-,10-,13+/m1/s1
SMILES C[C@@H]1[C@@H](C=C2C(C)(C)CC=C[C@@]12C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   192.15 Volume:   219.809
?
Van der Waals volume.
Dense:   0.874 LogP:   2.626
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.568
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.504
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   10.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.585 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.652 Fsp3:   0.692
MCE-18:   36.818
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.263 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.261
?
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:   0.848 Promiscuous compounds:   0.521

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.049 MDCK Permeability:   -4.679
Pgp-inhibitor:   0.309 Pgp-substrate:   0.862
PAMPA:   0.843
?
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):   0.11
20% Bioavailability (F20%):   0.881 30% Bioavailability (F30%):   0.913
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.905 MRP1:   0.908
Plasma Protein Binding (PPB):   69.525% Volume Distribution (VD):   0.04
Fu: 31.622%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.884
OATP1B3 inhibitor:   0.713 BCRP inhibitor:   0.133
BSEP inhibitor:   0.727

ADMET: Metabolism

CYP1A2-inhibitor:   0.021 CYP1A2-substrate:   0.823
CYP2C19-inhibitor:   0.349 CYP2C19-substrate:   0.207
CYP2C9-inhibitor:   0.037 CYP2C9-substrate:   0.463
CYP2D6-inhibitor:   0.072 CYP2D6-substrate:   0.163
CYP3A4-inhibitor:   0.411 CYP3A4-substrate:   0.74
CYP2B6-substrate:   0.095 CYP2C8-inhibitor:   0.946
HLM stability:   0.901
?
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):  10.315 Half-life (T1/2):  0.81

ADMET: Toxicity

hERG Blockers:  0.056 hERG Blockers (10um):  0.253
Human Hepatotoxicity (H-HT):  0.45 Drug-induced Liver Injury (DILI):  0.555
AMES Toxicity:  0.642 Rat Oral Acute Toxicity:  0.752
Maximum Recommended Daily Dose:  0.81 Skin Sensitization:  0.88
Carcinogencity:  0.876 Eye Corrosion:  0.609
Eye Irritation:  0.985 Respiratory Toxicity:  0.939
Drug-induced Neurotoxicity:  0.627 Ototoxicity:  0.195
Hematotoxicity:  0.381 Drug-induced Nephrotoxicity:  0.728
Genotoxicity:  0.703 RPMI-8226 Immunitoxicity:  0.117
A549 Cytotoxicity:  0.159 Hek293 Cytotoxicity:  0.304
BCF:   2.419
?
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:   3.714
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.713
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.396
?
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
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)88887-1]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. DOI[10.1071/CH03175]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. PMID[10075753]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. PMID[10543913]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. South Georgia Islands, South Atlantic n.a. PMID[15026054]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO25391 Vitex glabrata Species Lamiaceae Eukaryota leaves Chantaburi Province, Thailand 2007-Nov PMID[19943620]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota twigs n.a. n.a. PMID[20058933]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. PMID[21504145]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24256484]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota young fruits Khokkhon, Tha Bo District, Nong Khai Province, Thailand 2011-Aug PMID[25651042]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota flowers Pakook, Muang District, Chiang Rai Province, Thailand 2013-Feb PMID[25651042]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[27128898]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[30074787]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota Leaves n.a. n.a. PMID[31860303]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. PMID[9748381]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25391 Vitex glabrata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25091 Samadera bidwillii Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5027 Peniophora polygonia Species Peniophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25625 Hymenophyllum recurvum Species Hymenophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22293 Bryobium hyacinthoides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25364 Didemnum candidum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18842 Gnaphalium gaudichaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23568 Guatteria pogonopus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22293 Bryobium hyacinthoides Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24077 Astragalus pterocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22761 Gentiana cruciata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25625 Hymenophyllum recurvum Species Hymenophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18842 Gnaphalium gaudichaudianum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13588 Sanguinaria canadensis Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25472 Garcinia cowa Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28887 Eupomatia laurina Species Eupomatiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14117 Diplodia sapinea Species Botryosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22780 Sphaeranthus africanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13767 Woodfordia fruticosa Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25145 Cydonia oblonga Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24512 Xestospongia testudinaria Species Petrosiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25046 Aplidium meridianum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5027 Peniophora polygonia Species Peniophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25091 Samadera bidwillii Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25700 Psiadia punctulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24745 Salvia cavaleriei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23568 Guatteria pogonopus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25416 Uncaria cordata Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25364 Didemnum candidum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24601 Rumex dentatus Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25391 Vitex glabrata Species Lamiaceae 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 NPC256024 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC256024 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