Natural Product: NPC312048

Natural Product IDNPC312048
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
MXEIKUWMKSYEII-XRHWURSXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 9807366
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001586] Biflavonoids and polyflavonoids

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 MXEIKUWMKSYEII-XRHWURSXSA-N
Standard InCHI InChI=1S/C30H22O10/c31-15-5-1-13(2-6-15)22-12-21(37)24-19(35)11-20(36)26(30(24)39-22)27-28(38)25-18(34)9-17(33)10-23(25)40-29(27)14-3-7-16(32)8-4-14/h1-11,22,27,29,31-36H,12H2/t22-,27-,29+/m1/s1
SMILES c1cc(ccc1[C@H]1CC(=O)c2c(cc(c([C@@H]3C(=O)c4c(cc(cc4O[C@H]3c3ccc(cc3)O)O)O)c2O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   542.12 Volume:   527.089
?
Van der Waals volume.
Dense:   1.029 LogP:   3.974
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.407
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.757
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   36.0
TPSA:   173.98
?
Topological Polar Surface Area.
H-Bond Acceptor:   10.0
H-Bond Donor:   6.0 Rings:   6.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.212 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.014 Fsp3:   0.133
MCE-18:   116.471
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.971 Fluc inhibitor:   0.558
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.308
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.664
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.509 Promiscuous compounds:   0.027

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.582 MDCK Permeability:   -4.824
Pgp-inhibitor:   0.885 Pgp-substrate:   0.257
PAMPA:   0.065
?
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%):   0.004 30% Bioavailability (F30%):   0.996
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.894
Plasma Protein Binding (PPB):   95.785% Volume Distribution (VD):   -0.204
Fu: 7.083%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.994
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   1.0
BSEP inhibitor:   0.982

ADMET: Metabolism

CYP1A2-inhibitor:   0.069 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.974
CYP2C9-inhibitor:   0.082 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.791 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.97
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
HLM stability:   0.852
?
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):  2.792 Half-life (T1/2):  2.335

ADMET: Toxicity

hERG Blockers:  0.146 hERG Blockers (10um):  0.528
Human Hepatotoxicity (H-HT):  0.939 Drug-induced Liver Injury (DILI):  0.498
AMES Toxicity:  0.633 Rat Oral Acute Toxicity:  0.849
Maximum Recommended Daily Dose:  0.971 Skin Sensitization:  0.979
Carcinogencity:  0.182 Eye Corrosion:  0.0
Eye Irritation:  0.986 Respiratory Toxicity:  0.928
Drug-induced Neurotoxicity:  0.659 Ototoxicity:  0.558
Hematotoxicity:  0.043 Drug-induced Nephrotoxicity:  0.682
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.194
A549 Cytotoxicity:  0.971 Hek293 Cytotoxicity:  0.985
BCF:   1.18
?
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:   4.108
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.675
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.29
?
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
NPO11682 Eusynstyela latericius Species Styelidae Eukaryota n.a. n.a. n.a. PMID[19505081]
NPO11682 Eusynstyela latericius Species Styelidae Eukaryota n.a. Hixson Island (2145.0' S, 15017.5' E); Percy Island Group in the Central Great Barrier Reef, Queensland, Australia; Rib Reef (1828.7' S, 14652.3' E) n.a. PMID[19505081]
NPO11682 Eusynstyela latericius Species Styelidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15065 Daniellia ogea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14421 Vellozia compacta Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13172 Xylaria telfairii Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10893 Polyporus ciliatus Species Polyporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13664 Garcinia prainiana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14421 Vellozia compacta Species Velloziaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4680 Neatostema apulum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15065 Daniellia ogea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9336 Rhodococcus jostii Species Nocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11682 Eusynstyela latericius Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17151 Schizaphis graminum Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13172 Xylaria telfairii Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10893 Polyporus ciliatus Species Polyporaceae 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 NPC312048 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
1.0 High Similarity NPC69531
0.9032 High Similarity NPC224851
0.8358 Intermediate Similarity NPC479054
0.6912 Remote Similarity NPC63438
0.661 Remote Similarity NPC32441
0.661 Remote Similarity NPC79943
0.6533 Remote Similarity NPC475184
0.6528 Remote Similarity NPC186847
0.6145 Remote Similarity NPC168789
0.6104 Remote Similarity NPC75827
0.6066 Remote Similarity NPC603284
0.5781 Remote Similarity NPC321011
0.5781 Remote Similarity NPC294852
0.5781 Remote Similarity NPC188679
0.5588 Remote Similarity NPC480991
0.5556 Remote Similarity NPC243083
0.5556 Remote Similarity NPC13768
0.5556 Remote Similarity NPC287246
0.5507 Remote Similarity NPC107572
0.5507 Remote Similarity NPC32739
0.5441 Remote Similarity NPC236637
0.5429 Remote Similarity NPC477841
0.5385 Remote Similarity NPC274784
0.5385 Remote Similarity NPC20709
0.5312 Remote Similarity NPC295261
0.5312 Remote Similarity NPC296490
0.52 Remote Similarity NPC611447
0.5156 Remote Similarity NPC182421
0.5152 Remote Similarity NPC300668
0.5152 Remote Similarity NPC324386
0.5139 Remote Similarity NPC109223
0.5139 Remote Similarity NPC220998
0.5139 Remote Similarity NPC10937
0.5128 Remote Similarity NPC600882

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC312048 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
0.661 Remote Similarity NPD1552 Clinical (unspecified phase)
0.5556 Remote Similarity NPD1550 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