Natural Product: NPC470214

Natural Product IDNPC470214
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (3S,5S)-3-Acetoxy-5-Hydroxy-1-(3,4-Dihydroxyphenyl)-7-(4-Hydroxyphenyl)Heptane
IUPAC Name [(3S,5S)-1-(3,4-dihydroxyphenyl)-5-hydroxy-7-(4-hydroxyphenyl)heptan-3-yl] acetate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1824576
PubChem CID 54577124
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002650] Diarylheptanoids
        • [CHEMONTID:0002651] Linear diarylheptanoids

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 WFGFERPBWVNUAJ-OALUTQOASA-N
Standard InCHI InChI=1S/C21H26O6/c1-14(22)27-19(10-5-16-6-11-20(25)21(26)12-16)13-18(24)9-4-15-2-7-17(23)8-3-15/h2-3,6-8,11-12,18-19,23-26H,4-5,9-10,13H2,1H3/t18-,19-/m0/s1
SMILES O[C@H](C[C@@H](OC(=O)C)CCc1ccc(c(c1)O)O)CCc1ccc(cc1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   374.17 Volume:   388.945
?
Van der Waals volume.
Dense:   0.962 LogP:   1.849
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.952
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.279
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   13.0
TPSA:   107.22
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.397 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.121 Fsp3:   0.381
MCE-18:   28.0
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.556 Fluc inhibitor:   0.206
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.028
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.255
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.563 Promiscuous compounds:   0.427

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.337 MDCK Permeability:   -4.881
Pgp-inhibitor:   0.814 Pgp-substrate:   0.976
PAMPA:   0.233
?
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%):   0.989 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.061
Plasma Protein Binding (PPB):   68.209% Volume Distribution (VD):   -0.461
Fu: 29.305%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.961 BCRP inhibitor:   0.905
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.001
CYP2C19-inhibitor:   0.016 CYP2C19-substrate:   0.004
CYP2C9-inhibitor:   0.005 CYP2C9-substrate:   0.097
CYP2D6-inhibitor:   0.716 CYP2D6-substrate:   0.946
CYP3A4-inhibitor:   0.057 CYP3A4-substrate:   0.006
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.993
?
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):  13.598 Half-life (T1/2):  1.568

ADMET: Toxicity

hERG Blockers:  0.407 hERG Blockers (10um):  0.851
Human Hepatotoxicity (H-HT):  0.68 Drug-induced Liver Injury (DILI):  0.187
AMES Toxicity:  0.206 Rat Oral Acute Toxicity:  0.028
Maximum Recommended Daily Dose:  0.907 Skin Sensitization:  0.982
Carcinogencity:  0.238 Eye Corrosion:  0.011
Eye Irritation:  0.874 Respiratory Toxicity:  0.051
Drug-induced Neurotoxicity:  0.138 Ototoxicity:  0.773
Hematotoxicity:  0.03 Drug-induced Nephrotoxicity:  0.738
Genotoxicity:  0.344 RPMI-8226 Immunitoxicity:  0.019
A549 Cytotoxicity:  0.728 Hek293 Cytotoxicity:  0.566
BCF:   0.712
?
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:   3.522
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.787
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.348
?
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
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. rhizome n.a. DOI[10.1021/np100392m]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota Rhizomes n.a. n.a. PMID[20879743]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[21807513]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22741 Curcuma kwangsiensis Species Zingiberaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 9520.0 nM PMID[9784156]

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 NPC470214 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 NPC470215
0.9149 High Similarity NPC109371
0.8723 High Similarity NPC63345
0.74 Intermediate Similarity NPC86198
0.6727 Remote Similarity NPC200988
0.6727 Remote Similarity NPC145023
0.66 Remote Similarity NPC70084
0.6364 Remote Similarity NPC25689
0.6349 Remote Similarity NPC79715
0.6349 Remote Similarity NPC108659
0.6296 Remote Similarity NPC265454
0.6 Remote Similarity NPC610
0.6 Remote Similarity NPC179002
0.6 Remote Similarity NPC257430
0.6 Remote Similarity NPC175799
0.5714 Remote Similarity NPC231607
0.5556 Remote Similarity NPC34634
0.5455 Remote Similarity NPC226401
0.5455 Remote Similarity NPC158325
0.5455 Remote Similarity NPC174096
0.5455 Remote Similarity NPC193018
0.5397 Remote Similarity NPC160854
0.5397 Remote Similarity NPC469704
0.5397 Remote Similarity NPC469703
0.5273 Remote Similarity NPC75039
0.5273 Remote Similarity NPC98305
0.52 Remote Similarity NPC187583
0.5185 Remote Similarity NPC177576
0.5085 Remote Similarity NPC153795
0.5085 Remote Similarity NPC42911
0.5079 Remote Similarity NPC135464
0.5079 Remote Similarity NPC92623

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC470214 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