Natural Product: NPC316860

Natural Product IDNPC316860
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VUGRLRAUZWGZJP-JWFOYSBNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 59991339
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0003533] Flavonoid-7-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 VUGRLRAUZWGZJP-JWFOYSBNSA-N
Standard InCHI InChI=1S/C21H20O11/c22-7-14-17(26)19(28)20(29)21(32-14)31-13-6-12-15(18(27)16(13)25)10(24)5-11(30-12)8-1-3-9(23)4-2-8/h1-6,14,17,19-23,25-29H,7H2/t14-,17-,19+,20-,21?/m1/s1
SMILES C1=CC(=CC=C1C2=CC(=O)C3=C(C(=C(C=C3O2)OC4C(C(C(C(O4)CO)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   448.1 Volume:   413.147
?
Van der Waals volume.
Dense:   1.085 LogP:   -0.153
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.917
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.755
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   190.28
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   7.0 Rings:   4.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.261 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.93 Fsp3:   0.286
MCE-18:   87.63
?
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:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.45 Fluc inhibitor:   0.11
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.963
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.863
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.291 Promiscuous compounds:   0.882

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.289 MDCK Permeability:   -5.046
Pgp-inhibitor:   0.0 Pgp-substrate:   0.573
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):   0.961
20% Bioavailability (F20%):   0.961 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.929
Plasma Protein Binding (PPB):   80.787% Volume Distribution (VD):   0.01
Fu: 18.052%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.034
OATP1B3 inhibitor:   0.952 BCRP inhibitor:   0.871
BSEP inhibitor:   0.024

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.398 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.124 CYP2D6-substrate:   0.02
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.924
HLM stability:   0.0
?
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):  3.804 Half-life (T1/2):  2.732

ADMET: Toxicity

hERG Blockers:  0.048 hERG Blockers (10um):  0.323
Human Hepatotoxicity (H-HT):  0.5 Drug-induced Liver Injury (DILI):  0.728
AMES Toxicity:  0.557 Rat Oral Acute Toxicity:  0.292
Maximum Recommended Daily Dose:  0.416 Skin Sensitization:  0.368
Carcinogencity:  0.389 Eye Corrosion:  0.0
Eye Irritation:  0.442 Respiratory Toxicity:  0.089
Drug-induced Neurotoxicity:  0.06 Ototoxicity:  0.834
Hematotoxicity:  0.048 Drug-induced Nephrotoxicity:  0.051
Genotoxicity:  0.871 RPMI-8226 Immunitoxicity:  0.058
A549 Cytotoxicity:  0.145 Hek293 Cytotoxicity:  0.696
BCF:   0.299
?
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:   2.722
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.368
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.532
?
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
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[2488968]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[2610694]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3477 Plantago asiatica Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3477 Plantago asiatica Species Plantaginaceae 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 NPC316860 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 NPC146792
0.8714 High Similarity NPC58716
0.8696 High Similarity NPC45618
0.7703 Intermediate Similarity NPC84265
0.7671 Intermediate Similarity NPC39360
0.7671 Intermediate Similarity NPC29763
0.7671 Intermediate Similarity NPC210003
0.7568 Intermediate Similarity NPC93337
0.7467 Intermediate Similarity NPC105025
0.7195 Intermediate Similarity NPC3583
0.7013 Intermediate Similarity NPC245014
0.6795 Remote Similarity NPC610763
0.6753 Remote Similarity NPC83283
0.675 Remote Similarity NPC43211
0.675 Remote Similarity NPC601144
0.6667 Remote Similarity NPC259152
0.6667 Remote Similarity NPC189142
0.6667 Remote Similarity NPC77660
0.6582 Remote Similarity NPC45638
0.6543 Remote Similarity NPC601710
0.6538 Remote Similarity NPC58053
0.6538 Remote Similarity NPC261866
0.65 Remote Similarity NPC201292
0.6463 Remote Similarity NPC311830
0.6463 Remote Similarity NPC602805
0.6456 Remote Similarity NPC95090
0.6456 Remote Similarity NPC27408
0.641 Remote Similarity NPC331652
0.6386 Remote Similarity NPC469931
0.6375 Remote Similarity NPC186807
0.6341 Remote Similarity NPC605067
0.6329 Remote Similarity NPC143851
0.6324 Remote Similarity NPC198826
0.622 Remote Similarity NPC191306
0.6145 Remote Similarity NPC22832
0.6098 Remote Similarity NPC27942
0.6049 Remote Similarity NPC297987
0.6049 Remote Similarity NPC168822
0.6049 Remote Similarity NPC323593
0.6049 Remote Similarity NPC203500
0.6047 Remote Similarity NPC472607
0.6024 Remote Similarity NPC609451
0.5976 Remote Similarity NPC24043
0.5952 Remote Similarity NPC243930
0.593 Remote Similarity NPC477848
0.5882 Remote Similarity NPC607707
0.5843 Remote Similarity NPC607513
0.5833 Remote Similarity NPC237435
0.5747 Remote Similarity NPC172807
0.5732 Remote Similarity NPC77672
0.5732 Remote Similarity NPC133671
0.5732 Remote Similarity NPC135391
0.5732 Remote Similarity NPC78263
0.5732 Remote Similarity NPC250069
0.5698 Remote Similarity NPC88023
0.5698 Remote Similarity NPC116458
0.5698 Remote Similarity NPC246943
0.5698 Remote Similarity NPC309025
0.5667 Remote Similarity NPC65003
0.5595 Remote Similarity NPC488080
0.5595 Remote Similarity NPC169977
0.5591 Remote Similarity NPC150767
0.5556 Remote Similarity NPC44931
0.5542 Remote Similarity NPC19709
0.5529 Remote Similarity NPC222936
0.5476 Remote Similarity NPC8573
0.5476 Remote Similarity NPC277205
0.5476 Remote Similarity NPC37919
0.5476 Remote Similarity NPC136042
0.5455 Remote Similarity NPC601586
0.5444 Remote Similarity NPC603300
0.5412 Remote Similarity NPC84362
0.5412 Remote Similarity NPC10807
0.5412 Remote Similarity NPC161881
0.5402 Remote Similarity NPC115760
0.5402 Remote Similarity NPC197285
0.5376 Remote Similarity NPC64051
0.5349 Remote Similarity NPC198324
0.5349 Remote Similarity NPC117260
0.5342 Remote Similarity NPC162313
0.5333 Remote Similarity NPC8856
0.5294 Remote Similarity NPC145038
0.5294 Remote Similarity NPC56077
0.5294 Remote Similarity NPC197896
0.5294 Remote Similarity NPC281131
0.5294 Remote Similarity NPC313163
0.5294 Remote Similarity NPC253662
0.5294 Remote Similarity NPC179950
0.5294 Remote Similarity NPC88789
0.5294 Remote Similarity NPC491374
0.5287 Remote Similarity NPC168584
0.5287 Remote Similarity NPC307938
0.5287 Remote Similarity NPC285197
0.5287 Remote Similarity NPC488071
0.5281 Remote Similarity NPC488072
0.5278 Remote Similarity NPC275722
0.5258 Remote Similarity NPC298171
0.5233 Remote Similarity NPC181712
0.5227 Remote Similarity NPC284960
0.5227 Remote Similarity NPC486578
0.5222 Remote Similarity NPC4390
0.5213 Remote Similarity NPC64425
0.5208 Remote Similarity NPC270675
0.5208 Remote Similarity NPC195685
0.5205 Remote Similarity NPC57030
0.5176 Remote Similarity NPC289667
0.5176 Remote Similarity NPC110349
0.5172 Remote Similarity NPC182045
0.5172 Remote Similarity NPC205076
0.5172 Remote Similarity NPC21100
0.5169 Remote Similarity NPC605784
0.5155 Remote Similarity NPC256760
0.5116 Remote Similarity NPC105511
0.5116 Remote Similarity NPC161749
0.5116 Remote Similarity NPC609879
0.5114 Remote Similarity NPC282169
0.5114 Remote Similarity NPC60735
0.5114 Remote Similarity NPC26230
0.5111 Remote Similarity NPC203050
0.5111 Remote Similarity NPC225434
0.5111 Remote Similarity NPC190003
0.5106 Remote Similarity NPC122809
0.5102 Remote Similarity NPC101636
0.51 Remote Similarity NPC599948
0.5059 Remote Similarity NPC473043
0.5057 Remote Similarity NPC603655
0.5056 Remote Similarity NPC101026
0.5056 Remote Similarity NPC21666
0.5056 Remote Similarity NPC488077
0.5056 Remote Similarity NPC609478
0.5054 Remote Similarity NPC47923
0.5051 Remote Similarity NPC472994

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC316860 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
0.5833 Remote Similarity NPD4338 Clinical (unspecified phase)
0.5116 Remote Similarity NPD4381 Clinical (unspecified phase)

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