Natural Product: NPC214957

Natural Product IDNPC214957
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FWDXZNKYDTXGOT-XQRVVYSFSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 91715816
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 FWDXZNKYDTXGOT-XQRVVYSFSA-N
Standard InCHI InChI=1S/C21H24O5/c1-25-20-13-15(8-11-18(20)23)5-3-4-6-17(22)10-7-16-9-12-19(24)21(14-16)26-2/h4,6,8-9,11-14,23-24H,3,5,7,10H2,1-2H3/b6-4-
SMILES COc1cc(CC/C=CC(=O)CCc2ccc(c(c2)OC)O)ccc1O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   356.16 Volume:   377.519
?
Van der Waals volume.
Dense:   0.943 LogP:   2.529
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.572
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.869
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   14.0
TPSA:   75.99
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.668 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.341 Fsp3:   0.286
MCE-18:   13.0
?
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:   0
Colloidal aggregators:   0.465 Fluc inhibitor:   0.063
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.018
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.614
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.664 Promiscuous compounds:   0.058

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.234 MDCK Permeability:   -4.827
Pgp-inhibitor:   0.998 Pgp-substrate:   0.028
PAMPA:   0.002
?
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):   0.004
20% Bioavailability (F20%):   0.303 30% Bioavailability (F30%):   0.723
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.015
Plasma Protein Binding (PPB):   98.402% Volume Distribution (VD):   -0.294
Fu: 1.425%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.994
OATP1B3 inhibitor:   0.982 BCRP inhibitor:   0.288
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.969
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.999
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.066
CYP2D6-inhibitor:   0.828 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.932 CYP3A4-substrate:   0.958
CYP2B6-substrate:   0.005 CYP2C8-inhibitor:   1.0
HLM stability:   0.904
?
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):  7.163 Half-life (T1/2):  1.002

ADMET: Toxicity

hERG Blockers:  0.551 hERG Blockers (10um):  0.851
Human Hepatotoxicity (H-HT):  0.577 Drug-induced Liver Injury (DILI):  0.007
AMES Toxicity:  0.356 Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.227 Skin Sensitization:  0.997
Carcinogencity:  0.052 Eye Corrosion:  0.289
Eye Irritation:  0.963 Respiratory Toxicity:  0.825
Drug-induced Neurotoxicity:  0.212 Ototoxicity:  0.354
Hematotoxicity:  0.037 Drug-induced Nephrotoxicity:  0.564
Genotoxicity:  0.006 RPMI-8226 Immunitoxicity:  0.085
A549 Cytotoxicity:  0.53 Hek293 Cytotoxicity:  0.533
BCF:   1.513
?
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:   4.181
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.163
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.73
?
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
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[18177011]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[19271742]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[32872604]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[36352904]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[39679248]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[39680258]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[8064299]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Rhizome n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]

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 NPC214957 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 NPC5018
0.9091 High Similarity NPC123228
0.9091 High Similarity NPC123722
0.8889 High Similarity NPC179777
0.8 Intermediate Similarity NPC114298
0.7826 Intermediate Similarity NPC4181
0.7619 Intermediate Similarity NPC299406
0.75 Intermediate Similarity NPC164778
0.7347 Intermediate Similarity NPC257976
0.7347 Intermediate Similarity NPC273686
0.7347 Intermediate Similarity NPC242372
0.7347 Intermediate Similarity NPC312404
0.72 Intermediate Similarity NPC231572
0.6889 Remote Similarity NPC127937
0.6591 Remote Similarity NPC29989
0.6538 Remote Similarity NPC276466
0.6444 Remote Similarity NPC61062
0.64 Remote Similarity NPC303680
0.6327 Remote Similarity NPC481914
0.6279 Remote Similarity NPC8547
0.62 Remote Similarity NPC53305
0.6078 Remote Similarity NPC201777
0.6078 Remote Similarity NPC604524
0.6042 Remote Similarity NPC49529
0.6042 Remote Similarity NPC602856
0.5962 Remote Similarity NPC137427
0.5952 Remote Similarity NPC156840
0.5849 Remote Similarity NPC481913
0.5849 Remote Similarity NPC163083
0.5833 Remote Similarity NPC177291
0.5818 Remote Similarity NPC304622
0.5745 Remote Similarity NPC17943
0.5741 Remote Similarity NPC257589
0.5714 Remote Similarity NPC84076
0.5714 Remote Similarity NPC151167
0.5682 Remote Similarity NPC257124
0.5636 Remote Similarity NPC229497
0.5614 Remote Similarity NPC65935
0.5614 Remote Similarity NPC319282
0.5536 Remote Similarity NPC20287
0.5536 Remote Similarity NPC215941
0.5536 Remote Similarity NPC123196
0.5536 Remote Similarity NPC20404
0.5536 Remote Similarity NPC311419
0.5517 Remote Similarity NPC90128
0.551 Remote Similarity NPC312675
0.551 Remote Similarity NPC262156
0.551 Remote Similarity NPC184651
0.551 Remote Similarity NPC113865
0.5439 Remote Similarity NPC12022
0.5439 Remote Similarity NPC275724
0.5439 Remote Similarity NPC244246
0.5439 Remote Similarity NPC278308
0.5439 Remote Similarity NPC611247
0.5385 Remote Similarity NPC74817
0.5333 Remote Similarity NPC151405
0.5294 Remote Similarity NPC51840
0.5294 Remote Similarity NPC82679
0.5283 Remote Similarity NPC159968
0.5217 Remote Similarity NPC221049
0.5217 Remote Similarity NPC140359
0.5208 Remote Similarity NPC603326
0.5185 Remote Similarity NPC282000
0.5185 Remote Similarity NPC343720
0.5185 Remote Similarity NPC54872
0.5106 Remote Similarity NPC165133
0.5106 Remote Similarity NPC242885
0.5106 Remote Similarity NPC95614
0.5106 Remote Similarity NPC471693
0.5106 Remote Similarity NPC193544
0.5106 Remote Similarity NPC232316
0.5094 Remote Similarity NPC473853
0.5094 Remote Similarity NPC98631
0.5094 Remote Similarity NPC206615
0.5094 Remote Similarity NPC470212

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC214957 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
0.5682 Remote Similarity NPD228 Phase 0

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