Natural Product: NPC196512

Natural Product IDNPC196512
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YMGFTDKNIWPMGF-DXBMJSKRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 9913656
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000253] Stilbenes

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 YMGFTDKNIWPMGF-DXBMJSKRSA-N
Standard InCHI InChI=1S/C26H22O10/c27-18-7-2-14(11-21(18)30)1-6-17-16(4-9-20(29)25(17)33)5-10-24(32)36-23(26(34)35)13-15-3-8-19(28)22(31)12-15/h1-12,23,27-31,33H,13H2,(H,34,35)/b6-1+,10-5-/t23-/m0/s1
SMILES C(=Cc1c(ccc(c1O)O)/C=CC(=O)O[C@@H](Cc1ccc(c(c1)O)O)C(=O)O)/c1ccc(c(c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   494.12 Volume:   486.211
?
Van der Waals volume.
Dense:   1.016 LogP:   2.409
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.072
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.367
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   22.0
TPSA:   184.98
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   7.0 Rings:   3.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.106 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.387 Fsp3:   0.077
MCE-18:   44.0
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.988 Fluc inhibitor:   0.998
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.391
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.778
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.664 Promiscuous compounds:   0.555

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.626 MDCK Permeability:   -4.944
Pgp-inhibitor:   0.0 Pgp-substrate:   0.001
PAMPA:   0.999
?
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):   0.001
20% Bioavailability (F20%):   0.998 30% Bioavailability (F30%):   0.994
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.251
Plasma Protein Binding (PPB):   98.192% Volume Distribution (VD):   -0.66
Fu: 1.243%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.003

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.003 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.002 CYP2D6-substrate:   0.031
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.167
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.649
HLM stability:   0.34
?
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):  15.853 Half-life (T1/2):  2.243

ADMET: Toxicity

hERG Blockers:  0.043 hERG Blockers (10um):  0.265
Human Hepatotoxicity (H-HT):  0.544 Drug-induced Liver Injury (DILI):  0.838
AMES Toxicity:  0.351 Rat Oral Acute Toxicity:  0.183
Maximum Recommended Daily Dose:  0.699 Skin Sensitization:  1.0
Carcinogencity:  0.012 Eye Corrosion:  0.006
Eye Irritation:  0.961 Respiratory Toxicity:  0.172
Drug-induced Neurotoxicity:  0.004 Ototoxicity:  0.905
Hematotoxicity:  0.007 Drug-induced Nephrotoxicity:  0.586
Genotoxicity:  0.978 RPMI-8226 Immunitoxicity:  0.021
A549 Cytotoxicity:  0.959 Hek293 Cytotoxicity:  0.233
BCF:   0.941
?
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:   4.274
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.287
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.044
?
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
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[ 17014425]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1002/bab.1236]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2010.09.006]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)00169-2]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. stem n.a. DOI[10.1021/np50053a043]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[11374966]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. tuber n.a. PMID[12913245]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[1293938]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. fruit n.a. PMID[15128023]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[16038550]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[16181762]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[17217287]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17583950]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[18068204]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[18855446]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20455578]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21775156]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22223386]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota Lateral roots n.a. n.a. PMID[22607495]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22628040]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[22907155]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[23225552]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23286284]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[23707213]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[23707213]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[24108414]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[24793215]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[27569393]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. root n.a. PMID[27761113]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[29185738]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[30351923]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota Roots n.a. n.a. PMID[30892884]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. root n.a. PMID[3655791]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[8277309]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota roots n.a. n.a. PMID[9834151]
NPO29892 Musa paradisiaca Species Musaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29861 Aconitum carmichaeli Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO549 Musa X paradisiaca Strain Musaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO9632 Annona reticulata Species Annonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9632 Annona reticulata Species Annonaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO549 Musa X paradisiaca Strain Musaceae Eukaryota n.a. n.a. Database[FooDB]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29861 Aconitum carmichaeli Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29892 Musa paradisiaca Species Musaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO549 Musa X paradisiaca Strain Musaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29892 Musa paradisiaca Species Musaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29861 Aconitum carmichaeli Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5743 Salvia miltiorrhiza Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4902 Aconitum carmichaelii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25813 Salvia przewalskii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO549 Musa X paradisiaca Strain Musaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9632 Annona reticulata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15401 Theobroma cacao Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5743 Salvia miltiorrhiza Species Lamiaceae 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 NPC196512 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 NPC38473
0.7586 Intermediate Similarity NPC18074
0.7586 Intermediate Similarity NPC5419
0.7586 Intermediate Similarity NPC25581
0.7586 Intermediate Similarity NPC61
0.7049 Intermediate Similarity NPC198388
0.6176 Remote Similarity NPC289690
0.6029 Remote Similarity NPC486819
0.6027 Remote Similarity NPC160378
0.5667 Remote Similarity NPC217052
0.5667 Remote Similarity NPC329344
0.5667 Remote Similarity NPC237506
0.5667 Remote Similarity NPC32626
0.5513 Remote Similarity NPC41494
0.5513 Remote Similarity NPC186100
0.5513 Remote Similarity NPC189197
0.5507 Remote Similarity NPC179505
0.5484 Remote Similarity NPC278652
0.5443 Remote Similarity NPC272750
0.5385 Remote Similarity NPC251407
0.5385 Remote Similarity NPC168653
0.5231 Remote Similarity NPC132921
0.5185 Remote Similarity NPC301089
0.5139 Remote Similarity NPC156709
0.5139 Remote Similarity NPC279676

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC196512 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