Natural Product: NPC289006

Natural Product IDNPC289006
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 RWLCWWWLTRAVKI-MRVPVSSYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones

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 RWLCWWWLTRAVKI-MRVPVSSYSA-N
Standard InCHI InChI=1S/C18H14O8/c1-8(19)18(24)25-10-5-13(22)17-14(23)7-15(26-16(17)6-10)9-2-3-11(20)12(21)4-9/h2-8,19-22H,1H3/t8-/m1/s1
SMILES C[C@H](C(=O)Oc1cc(c2c(=O)cc(c3ccc(c(c3)O)O)oc2c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   358.07 Volume:   340.809
?
Van der Waals volume.
Dense:   1.051 LogP:   1.719
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.633
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.945
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   19.0
TPSA:   137.43
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.316 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.067 Fsp3:   0.111
MCE-18:   40.0
?
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:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.545 Fluc inhibitor:   0.745
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.982
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.472
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.338 Promiscuous compounds:   0.597

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.357 MDCK Permeability:   -4.8
Pgp-inhibitor:   0.033 Pgp-substrate:   0.061
PAMPA:   0.797
?
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):   0.298
20% Bioavailability (F20%):   0.986 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.891
Plasma Protein Binding (PPB):   90.279% Volume Distribution (VD):   -0.221
Fu: 10.737%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.953
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.875
BSEP inhibitor:   0.657

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.001
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.147
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.005
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.991
HLM stability:   0.577
?
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):  8.226 Half-life (T1/2):  1.443

ADMET: Toxicity

hERG Blockers:  0.03 hERG Blockers (10um):  0.356
Human Hepatotoxicity (H-HT):  0.359 Drug-induced Liver Injury (DILI):  0.81
AMES Toxicity:  0.376 Rat Oral Acute Toxicity:  0.277
Maximum Recommended Daily Dose:  0.758 Skin Sensitization:  0.915
Carcinogencity:  0.223 Eye Corrosion:  0.127
Eye Irritation:  0.985 Respiratory Toxicity:  0.35
Drug-induced Neurotoxicity:  0.006 Ototoxicity:  0.258
Hematotoxicity:  0.047 Drug-induced Nephrotoxicity:  0.042
Genotoxicity:  0.955 RPMI-8226 Immunitoxicity:  0.028
A549 Cytotoxicity:  0.232 Hek293 Cytotoxicity:  0.333
BCF:   0.847
?
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:   3.556
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.732
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.291
?
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
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. leaf n.a. PMID[14709876]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. twig n.a. PMID[14709876]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota Leaves; Twigs n.a. n.a. PMID[15043402]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota stem wood n.a. n.a. PMID[16180806]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. PMID[16309320]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota leaves n.a. n.a. PMID[16792412]
NPO23769 Ainsliaea macrocephala Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[18484734]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[18489163]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19128011]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota leaves and stems Kunming, Yunnan, China 2007-AUG PMID[19133780]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[31475763]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[31983544]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32092043]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36866384]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36929733]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37151483]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[38931446]
NPO21352 Boronia ternata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23721 Epidendrum rigidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24993 Conospermum teretifolium Species Proteaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23849 Dicoma anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24462 Pityrogramma ebenea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24952 Galeopsis tetrahit Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23896 Cytisus ratisbonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21478 Buxus hyrcana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25037 Nepeta cataria Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21352 Boronia ternata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23302 Strychnos camptoneura Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24015 Perknaster fuscus Species Ganeriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24258 Vellozia nivea Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23769 Ainsliaea macrocephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23849 Dicoma anomala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24301 Buxus microphylla Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21478 Buxus hyrcana Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23896 Cytisus ratisbonensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25080 Sphaeria maculans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO18735 Pinus mugo Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24952 Galeopsis tetrahit Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23930 Luculia pinceana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24462 Pityrogramma ebenea Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28748 Aphis sambuci Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23473 Cinnamomum kotoense Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24993 Conospermum teretifolium Species Proteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23428 Tinus mamillata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20498 Cephalaria ambrosioides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23474 Abies veitchii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22684 Enrichment culture Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO23264 Marrubium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18918 Lecanicillium muscarium Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24498 Casearia membranacea Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23721 Epidendrum rigidum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23557 Zanthoxylum ailanthoides Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7197 Colchicum robustum Species Colchicaceae 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 NPC289006 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
0.7586 Intermediate Similarity NPC108406
0.6528 Remote Similarity NPC19709
0.6364 Remote Similarity NPC190003
0.629 Remote Similarity NPC234133
0.625 Remote Similarity NPC223579
0.6216 Remote Similarity NPC189142
0.6216 Remote Similarity NPC77660
0.6129 Remote Similarity NPC29353
0.5974 Remote Similarity NPC20505
0.5909 Remote Similarity NPC137062
0.5873 Remote Similarity NPC127447
0.5783 Remote Similarity NPC210073
0.5758 Remote Similarity NPC195202
0.5735 Remote Similarity NPC605587
0.5692 Remote Similarity NPC25270
0.5692 Remote Similarity NPC162313
0.561 Remote Similarity NPC8856
0.561 Remote Similarity NPC606546
0.5538 Remote Similarity NPC33265
0.5538 Remote Similarity NPC48479
0.5538 Remote Similarity NPC87125
0.5538 Remote Similarity NPC188871
0.5529 Remote Similarity NPC115674
0.5526 Remote Similarity NPC473043
0.5526 Remote Similarity NPC331652
0.5522 Remote Similarity NPC177298
0.5517 Remote Similarity NPC229409
0.5443 Remote Similarity NPC27942
0.5402 Remote Similarity NPC65711
0.5397 Remote Similarity NPC279121
0.5373 Remote Similarity NPC153758
0.5352 Remote Similarity NPC602829
0.5303 Remote Similarity NPC100887
0.5294 Remote Similarity NPC124784
0.5278 Remote Similarity NPC476283
0.5275 Remote Similarity NPC484301
0.527 Remote Similarity NPC473241
0.5256 Remote Similarity NPC39360
0.5256 Remote Similarity NPC29763
0.5256 Remote Similarity NPC210003
0.5224 Remote Similarity NPC605047
0.5195 Remote Similarity NPC158027
0.5195 Remote Similarity NPC600396
0.5185 Remote Similarity NPC282169
0.5128 Remote Similarity NPC159707
0.5125 Remote Similarity NPC181712
0.5122 Remote Similarity NPC22832
0.5122 Remote Similarity NPC80188
0.5075 Remote Similarity NPC188203
0.5065 Remote Similarity NPC603508
0.5063 Remote Similarity NPC121649
0.506 Remote Similarity NPC220169

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC289006 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
0.5397 Remote Similarity NPD1511 Phase 2

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