Natural Product: NPC167551

Natural Product IDNPC167551
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HAKDYPJVGUKNJQ-KTAJNNJTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5317432
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004144] Heteroaromatic compounds

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 HAKDYPJVGUKNJQ-KTAJNNJTSA-N
Standard InCHI InChI=1S/C12H8OS/c1(5-11-6-3-9-13-11)2-7-12-8-4-10-14-12/h1,3-6,8-10H/b5-1-
SMILES C(=Cc1ccco1)C#Cc1cccs1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   200.03 Volume:   207.839
?
Van der Waals volume.
Dense:   0.962 LogP:   3.2
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.721
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.512
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   12.0
TPSA:   13.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.643 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.985 Fsp3:   0.0
MCE-18:   8.0
?
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:   0.108 Fluc inhibitor:   0.977
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.024
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.403
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.997 Promiscuous compounds:   0.005

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.3 MDCK Permeability:   -4.643
Pgp-inhibitor:   0.962 Pgp-substrate:   0.0
PAMPA:   0.041
?
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):   0.222
20% Bioavailability (F20%):   0.607 30% Bioavailability (F30%):   0.428
50% Bioavailability (F50%):   0.698

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.08 MRP1:   0.009
Plasma Protein Binding (PPB):   98.266% Volume Distribution (VD):   -0.077
Fu: 0.978%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.199
OATP1B3 inhibitor:   0.799 BCRP inhibitor:   0.001
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.033 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.377 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.999 CYP2C9-substrate:   0.317
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.777
CYP3A4-inhibitor:   0.015 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.012 CYP2C8-inhibitor:   1.0
HLM stability:   0.035
?
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):  8.134 Half-life (T1/2):  0.63

ADMET: Toxicity

hERG Blockers:  0.157 hERG Blockers (10um):  0.466
Human Hepatotoxicity (H-HT):  0.387 Drug-induced Liver Injury (DILI):  0.971
AMES Toxicity:  0.567 Rat Oral Acute Toxicity:  0.659
Maximum Recommended Daily Dose:  0.169 Skin Sensitization:  0.758
Carcinogencity:  0.611 Eye Corrosion:  0.987
Eye Irritation:  0.989 Respiratory Toxicity:  0.983
Drug-induced Neurotoxicity:  0.112 Ototoxicity:  0.301
Hematotoxicity:  0.054 Drug-induced Nephrotoxicity:  0.181
Genotoxicity:  0.691 RPMI-8226 Immunitoxicity:  0.033
A549 Cytotoxicity:  0.058 Hek293 Cytotoxicity:  0.236
BCF:   1.675
?
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:   4.075
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.163
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.821
?
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
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[ 16712885]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.foodchem.2013.08.121]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Flowers n.a. n.a. PMID[16180814]
NPO8258 Camellia sinensis Species Theaceae Eukaryota seeds Shizuoka prefecture, Japan n.a. PMID[16499314]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[21434603]
NPO11629 Brassica nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21861458]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. flower n.a. PMID[21922925]
NPO8258 Camellia sinensis Species Theaceae Eukaryota flower buds n.a. n.a. PMID[21925888]
NPO8258 Camellia sinensis Species Theaceae Eukaryota leaves n.a. n.a. PMID[22377672]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. leaf n.a. PMID[23265489]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaves Bandung, West Java, Indonesia PMID[23621359]
NPO25014 Achillea millefolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36905473]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. PMID[37255739]
NPO15577 Volvariella volvacea Species Pluteaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25014 Achillea millefolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18546 Senna longiracemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19200 Rolandra fruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15940 Pinus gerardiana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18798 Parmelia perlata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19655 Larix sukaczewii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18201 Gonimbrasia belina n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO19109 Cetraria sanguinea Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18469 Anochetus mayri Species Formicidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11629 Brassica nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11629 Brassica nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25014 Achillea millefolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11629 Brassica nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25014 Achillea millefolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15577 Volvariella volvacea Species Pluteaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25014 Achillea millefolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18469 Anochetus mayri Species Formicidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15940 Pinus gerardiana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8258 Camellia sinensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18201 Gonimbrasia belina n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO25014 Achillea millefolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11629 Brassica nigra Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20513 Codium fragile Species Codiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19200 Rolandra fruticosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19109 Cetraria sanguinea Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15577 Volvariella volvacea Species Pluteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18798 Parmelia perlata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18546 Senna longiracemosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19655 Larix sukaczewii Species Pinaceae 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 NPC167551 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
0.561 Remote Similarity NPC219651

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC167551 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