Natural Product: NPC482521

Natural Product IDNPC482521
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
UYBJDEJISDOBSX-ISZOUKDZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 122194859
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003531] Flavonoid-3-O-glycosides

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 UYBJDEJISDOBSX-ISZOUKDZSA-N
Standard InCHI InChI=1S/C56H64O31/c1-18-37(66)41(70)45(74)54(81-18)79-16-32-39(68)43(72)47(76)56(83-32)87-52-40(69)36-31(64)15-30(63)35(51(36)86-49(52)22-5-7-25(58)27(60)13-22)23-14-29(62)28(61)12-21(23)9-10-78-53-48(77)44(73)50(85-34(65)8-4-20-3-6-24(57)26(59)11-20)33(84-53)17-80-55-46(75)42(71)38(67)19(2)82-55/h3-8,11-15,18-19,32-33,37-39,41-48,50,53-64,66-68,70-77H,9-10,16-17H2,1-2H3/b8-4+/t18-,19-,32+,33+,37-,38-,39+,41+,42+,43-,44+,45+,46+,47+,48+,50+,53+,54+,55+,56-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@@H](O2)Oc2c(=O)c3c(cc(c(c4cc(c(cc4CCO[C@H]4[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]5[C@@H]([C@@H]([C@H]([C@H](C)O5)O)O)O)O4)OC(=O)/C=C/c4ccc(c(c4)O)O)O)O)O)O)c3oc2c2ccc(c(c2)O)O)O)O)O)O)O)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1232.34 Volume:   1130.437
?
Van der Waals volume.
Dense:   1.09 LogP:   0.235
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.653
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.711
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   18.0 Rigid Bonds:   56.0
TPSA:   514.72
?
Topological Polar Surface Area.
H-Bond Acceptor:   31.0
H-Bond Donor:   19.0 Rings:   9.0
Heavy Atoms:   31.0

MedChem Properties

QED Drug-Likeness Score:   0.026 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.838 Fsp3:   0.464
MCE-18:   230.195
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.687 Fluc inhibitor:   0.364
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.799
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.667
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.334 Promiscuous compounds:   0.575

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.845 MDCK Permeability:   -5.002
Pgp-inhibitor:   0.0 Pgp-substrate:   0.817
PAMPA:   1.0
?
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):   0.974
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.001
Plasma Protein Binding (PPB):   77.717% Volume Distribution (VD):   0.043
Fu: 17.184%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.015
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.613
?
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):  0.216 Half-life (T1/2):  8.103

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.226
Human Hepatotoxicity (H-HT):  0.435 Drug-induced Liver Injury (DILI):  0.996
AMES Toxicity:  0.974 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.018 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.006 Drug-induced Nephrotoxicity:  0.396
Genotoxicity:  0.893 RPMI-8226 Immunitoxicity:  0.139
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.702
BCF:   0.432
?
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:   3.408
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.979
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.441
?
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
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[17156960]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[26422318]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota Fruits n.a. n.a. PMID[28218000]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21387 Forsythia suspensa Species Oleaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21387 Forsythia suspensa Species Oleaceae 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
NPT681 Cell line PC-12 Rattus norvegicus Activity = 64.0 % PMID[26422318]
NPT681 Cell line PC-12 Rattus norvegicus Activity = 96.2 % PMID[26422318]
NPT681 Cell line PC-12 Rattus norvegicus Activity = 93.2 % PMID[26422318]
NPT681 Cell line PC-12 Rattus norvegicus Activity = 75.5 % PMID[26422318]
NPT681 Cell line PC-12 Rattus norvegicus Activity = 54.3 % PMID[26422318]
NPT681 Cell line PC-12 Rattus norvegicus Activity = 67.9 % PMID[26422318]

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 NPC482521 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
0.6765 Remote Similarity NPC482520
0.6765 Remote Similarity NPC482519
0.6587 Remote Similarity NPC156785
0.6043 Remote Similarity NPC97817
0.5985 Remote Similarity NPC241781
0.5954 Remote Similarity NPC474522
0.592 Remote Similarity NPC81042
0.5755 Remote Similarity NPC30011
0.5755 Remote Similarity NPC72554
0.5714 Remote Similarity NPC162394
0.5702 Remote Similarity NPC203259
0.5702 Remote Similarity NPC33054
0.5702 Remote Similarity NPC176740
0.5702 Remote Similarity NPC471725
0.5702 Remote Similarity NPC134532
0.5702 Remote Similarity NPC602582
0.5547 Remote Similarity NPC214621
0.5547 Remote Similarity NPC34267
0.55 Remote Similarity NPC275977
0.5469 Remote Similarity NPC223426
0.5424 Remote Similarity NPC81515
0.539 Remote Similarity NPC231787
0.536 Remote Similarity NPC126784
0.536 Remote Similarity NPC241423
0.5299 Remote Similarity NPC139571
0.5242 Remote Similarity NPC173582
0.5242 Remote Similarity NPC265885
0.5242 Remote Similarity NPC181465
0.5242 Remote Similarity NPC215710
0.5242 Remote Similarity NPC473438
0.5242 Remote Similarity NPC253788
0.52 Remote Similarity NPC156869
0.5194 Remote Similarity NPC473073
0.5156 Remote Similarity NPC473327
0.512 Remote Similarity NPC39834
0.5115 Remote Similarity NPC470446
0.5103 Remote Similarity NPC223860
0.5078 Remote Similarity NPC470443
0.5077 Remote Similarity NPC476472
0.5077 Remote Similarity NPC294815
0.5077 Remote Similarity NPC85751
0.5077 Remote Similarity NPC16194
0.5077 Remote Similarity NPC19240
0.5068 Remote Similarity NPC487502
0.5034 Remote Similarity NPC249560

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC482521 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
0.5702 Remote Similarity NPD6797 Phase 2
0.5194 Remote Similarity NPD7251 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