Natural Product: NPC258605

Natural Product IDNPC258605
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YGSPWCVTJRFZEL-UHFFFAOYSA-M
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 23677501
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0001290] Indolyl carboxylic acids and derivatives
          • [CHEMONTID:0001252] Indole-3-acetic acid derivatives

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 YGSPWCVTJRFZEL-UHFFFAOYSA-M
Standard InCHI InChI=1S/C10H9NO2.Na/c12-10(13)5-7-6-11-9-4-2-1-3-8(7)9;/h1-4,6,11H,5H2,(H,12,13);/q;+1/p-1
SMILES c1ccc2c(c1)c(CC(=O)[O-])c[nH]2.[Na+]

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   174.06 Volume:   178.48
?
Van der Waals volume.
Dense:   0.975 LogP:   0.289
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.254
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.923
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   11.0
TPSA:   55.92
?
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:   0.719 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.455 Fsp3:   0.1
MCE-18:   10.0
?
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:   0.072 Fluc inhibitor:   0.031
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.046
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.164
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.345 Promiscuous compounds:   0.474

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.635 MDCK Permeability:   -4.2
Pgp-inhibitor:   0.0 Pgp-substrate:   0.001
PAMPA:   0.931
?
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%):   0.001 30% Bioavailability (F30%):   0.001
50% Bioavailability (F50%):   0.016

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.187 MRP1:   0.975
Plasma Protein Binding (PPB):   74.055% Volume Distribution (VD):   -0.148
Fu: 25.807%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.021
OATP1B3 inhibitor:   0.402 BCRP inhibitor:   0.0
BSEP inhibitor:   0.44

ADMET: Metabolism

CYP1A2-inhibitor:   0.017 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.335 CYP2C19-substrate:   0.069
CYP2C9-inhibitor:   0.572 CYP2C9-substrate:   0.009
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.207
CYP3A4-inhibitor:   0.479 CYP3A4-substrate:   0.002
CYP2B6-substrate:   0.008 CYP2C8-inhibitor:   0.892
HLM stability:   0.471
?
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):  1.742 Half-life (T1/2):  3.488

ADMET: Toxicity

hERG Blockers:  0.039 hERG Blockers (10um):  0.11
Human Hepatotoxicity (H-HT):  0.984 Drug-induced Liver Injury (DILI):  0.951
AMES Toxicity:  0.514 Rat Oral Acute Toxicity:  0.553
Maximum Recommended Daily Dose:  0.174 Skin Sensitization:  0.99
Carcinogencity:  0.38 Eye Corrosion:  0.34
Eye Irritation:  0.994 Respiratory Toxicity:  0.28
Drug-induced Neurotoxicity:  0.943 Ototoxicity:  0.867
Hematotoxicity:  0.805 Drug-induced Nephrotoxicity:  0.547
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.011
A549 Cytotoxicity:  0.001 Hek293 Cytotoxicity:  0.018
BCF:   0.839
?
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:   3.395
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.405
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.015
?
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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. DOI[10.1111/j.1365-3040.1996.tb00393.x]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[18270436]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23793896]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. seed n.a. PMID[24967651]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[39053741]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO20824 Ecklonia kurome Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2837 Aloe spicata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20824 Ecklonia kurome Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20824 Ecklonia kurome Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14149 Saccharina japonica Species Laminariaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2837 Aloe spicata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20824 Ecklonia kurome Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22132 Hordeum vulgare Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9069 Persicaria tinctoria Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20824 Ecklonia kurome Species Lessoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2690 Carapichea ipecacuanha Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14149 Saccharina japonica Species Laminariaceae 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 NPC258605 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
0.6905 Remote Similarity NPC111275
0.561 Remote Similarity NPC601214
0.5476 Remote Similarity NPC300149
0.5476 Remote Similarity NPC42372
0.5476 Remote Similarity NPC230002
0.54 Remote Similarity NPC14113
0.54 Remote Similarity NPC145885
0.54 Remote Similarity NPC84827
0.525 Remote Similarity NPC261195
0.5238 Remote Similarity NPC216643
0.5238 Remote Similarity NPC288838
0.5116 Remote Similarity NPC105127
0.5116 Remote Similarity NPC53947
0.5116 Remote Similarity NPC102423
0.5111 Remote Similarity NPC230869
0.5111 Remote Similarity NPC138370
0.5111 Remote Similarity NPC279081
0.5102 Remote Similarity NPC78020

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC258605 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