Natural Product: NPC255392

Natural Product IDNPC255392
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XXVKJERGKQQVSX-MSOLQXFVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 15109631
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

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 XXVKJERGKQQVSX-MSOLQXFVSA-N
Standard InCHI InChI=1S/C18H16O6/c1-10(19)23-18-16(21)15-13(20)8-12(22-2)9-14(15)24-17(18)11-6-4-3-5-7-11/h3-9,17-18,20H,1-2H3/t17-,18+/m1/s1
SMILES CC(=O)O[C@H]1C(=O)c2c(cc(cc2O[C@@H]1c1ccccc1)OC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   328.09 Volume:   325.865
?
Van der Waals volume.
Dense:   1.007 LogP:   2.992
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.948
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.546
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   19.0
TPSA:   82.06
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.872 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.11 Fsp3:   0.222
MCE-18:   57.273
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.366 Fluc inhibitor:   0.62
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.295
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.296
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.397 Promiscuous compounds:   0.125

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.189 MDCK Permeability:   -4.673
Pgp-inhibitor:   0.999 Pgp-substrate:   0.034
PAMPA:   0.029
?
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):   0.022
20% Bioavailability (F20%):   0.017 30% Bioavailability (F30%):   0.577
50% Bioavailability (F50%):   0.789

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.075 MRP1:   0.332
Plasma Protein Binding (PPB):   94.539% Volume Distribution (VD):   0.069
Fu: 5.173%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.376
BSEP inhibitor:   0.918

ADMET: Metabolism

CYP1A2-inhibitor:   0.668 CYP1A2-substrate:   0.83
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.018
CYP2C9-inhibitor:   0.831 CYP2C9-substrate:   0.09
CYP2D6-inhibitor:   0.112 CYP2D6-substrate:   0.075
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.301
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.603
HLM stability:   0.029
?
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):  5.872 Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.088 hERG Blockers (10um):  0.386
Human Hepatotoxicity (H-HT):  0.773 Drug-induced Liver Injury (DILI):  0.87
AMES Toxicity:  0.761 Rat Oral Acute Toxicity:  0.355
Maximum Recommended Daily Dose:  0.235 Skin Sensitization:  0.926
Carcinogencity:  0.306 Eye Corrosion:  0.016
Eye Irritation:  0.892 Respiratory Toxicity:  0.352
Drug-induced Neurotoxicity:  0.498 Ototoxicity:  0.253
Hematotoxicity:  0.43 Drug-induced Nephrotoxicity:  0.8
Genotoxicity:  0.97 RPMI-8226 Immunitoxicity:  0.159
A549 Cytotoxicity:  0.26 Hek293 Cytotoxicity:  0.299
BCF:   1.073
?
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:   3.849
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.877
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.463
?
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
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[17548953]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota Aerial parts n.a. n.a. PMID[20166702]
NPO40884 Mexican propolis Species n.a. n.a. n.a. n.a. n.a. PMID[20307087]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. exocarp n.a. PMID[21114277]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. aerial part n.a. PMID[21171571]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[24675423]
NPO21665 Mycobacterium avium Species Mycobacteriaceae Bacteria n.a. n.a. n.a. PMID[2476400]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Bako, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Enemore, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Gedo, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Holleta, Ethiopia PMID[24926420]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. PMID[29094598]
NPO7848 Magnolia laevifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[37715638]
NPO14169 Acrocarpia paniculata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10418 Padina tetrastromatica Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21665 Mycobacterium avium Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO1030 Haplopappus remyanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7848 Magnolia laevifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40884 Mexican propolis Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9569 Licaria chrysophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7848 Magnolia laevifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14369 Pocillopora eydouxi Species Pocilloporidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4700 Pertusaria truncata Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12521 Sphaeranthus confertifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3013 Clathria basilana Species Microcionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5280 Rubia tetragona Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11842 Petasites laevigatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14470 Polypodium decumanum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14169 Acrocarpia paniculata Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13178 Ornithoglossum viride Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13876 Cedrela salvadorensis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13473 Anodendron affine Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9569 Licaria chrysophylla Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7848 Magnolia laevifolia Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13379 Schizanthus tricolor Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1030 Haplopappus remyanus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7541 Ormosia hosiei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13669 Hertia cheirifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21665 Mycobacterium avium Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10418 Padina tetrastromatica Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11266 Garcinia cambogia Species Clusiaceae 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 NPC255392 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
0.7925 Intermediate Similarity NPC112418
0.7222 Intermediate Similarity NPC609747
0.6545 Remote Similarity NPC471500
0.6316 Remote Similarity NPC471479
0.6071 Remote Similarity NPC122828
0.6066 Remote Similarity NPC295650
0.5667 Remote Similarity NPC471744
0.5614 Remote Similarity NPC150648
0.5079 Remote Similarity NPC471745

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC255392 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