Natural Product: NPC61104

Natural Product IDNPC61104
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SVZGCYLXISBVQK-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5318276
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0000190] Methoxyphenols
          • [CHEMONTID:0001706] Gingerdiols

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 SVZGCYLXISBVQK-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H24O4/c1-3-4-12(16)10-13(17)7-5-11-6-8-14(18)15(9-11)19-2/h6,8-9,12-13,16-18H,3-5,7,10H2,1-2H3
SMILES CCCC(CC(CCc1ccc(c(c1)OC)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   268.17 Volume:   286.691
?
Van der Waals volume.
Dense:   0.935 LogP:   2.268
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.207
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.696
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   6.0
TPSA:   69.92
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   1.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.676 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.869 Fsp3:   0.6
MCE-18:   16.0
?
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:   0.244 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.092
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.682 Promiscuous compounds:   0.666

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.026 MDCK Permeability:   -4.77
Pgp-inhibitor:   0.015 Pgp-substrate:   0.737
PAMPA:   0.323
?
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):   0.176
20% Bioavailability (F20%):   0.568 30% Bioavailability (F30%):   0.95
50% Bioavailability (F50%):   0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.066 MRP1:   0.48
Plasma Protein Binding (PPB):   75.172% Volume Distribution (VD):   0.112
Fu: 23.36%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.768
OATP1B3 inhibitor:   0.855 BCRP inhibitor:   0.479
BSEP inhibitor:   0.89

ADMET: Metabolism

CYP1A2-inhibitor:   0.062 CYP1A2-substrate:   0.026
CYP2C19-inhibitor:   0.981 CYP2C19-substrate:   0.003
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.101
CYP2D6-inhibitor:   0.347 CYP2D6-substrate:   0.021
CYP3A4-inhibitor:   0.639 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.969
HLM stability:   0.029
?
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):  12.089 Half-life (T1/2):  1.458

ADMET: Toxicity

hERG Blockers:  0.366 hERG Blockers (10um):  0.744
Human Hepatotoxicity (H-HT):  0.617 Drug-induced Liver Injury (DILI):  0.045
AMES Toxicity:  0.151 Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.47 Skin Sensitization:  0.746
Carcinogencity:  0.15 Eye Corrosion:  0.094
Eye Irritation:  0.817 Respiratory Toxicity:  0.474
Drug-induced Neurotoxicity:  0.127 Ototoxicity:  0.87
Hematotoxicity:  0.199 Drug-induced Nephrotoxicity:  0.702
Genotoxicity:  0.002 RPMI-8226 Immunitoxicity:  0.05
A549 Cytotoxicity:  0.195 Hek293 Cytotoxicity:  0.34
BCF:   0.51
?
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:   3.12
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.421
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.714
?
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19829679]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[20590154]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. root n.a. PMID[21087019]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22314230]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23521110]
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37569279]
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9834167]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota 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 Resin, Exudate, Sap 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 Root n.a. n.a. Database[FooDB]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28877 Scutellaria baicalensis 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 NPC61104 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
0.9091 High Similarity NPC311595
0.9091 High Similarity NPC24474
0.9 High Similarity NPC312675
0.9 High Similarity NPC262156
0.9 High Similarity NPC184651
0.9 High Similarity NPC113865
0.8182 Intermediate Similarity NPC473853
0.8182 Intermediate Similarity NPC98631
0.8182 Intermediate Similarity NPC206615
0.8182 Intermediate Similarity NPC470212
0.8 Intermediate Similarity NPC324571
0.7826 Intermediate Similarity NPC164386
0.7826 Intermediate Similarity NPC343720
0.7826 Intermediate Similarity NPC54872
0.6863 Remote Similarity NPC310718
0.6667 Remote Similarity NPC8547
0.66 Remote Similarity NPC137427
0.6458 Remote Similarity NPC186843
0.6275 Remote Similarity NPC470213
0.6111 Remote Similarity NPC20287
0.6111 Remote Similarity NPC215941
0.6111 Remote Similarity NPC123196
0.6111 Remote Similarity NPC20404
0.6111 Remote Similarity NPC311419
0.6087 Remote Similarity NPC299406
0.6071 Remote Similarity NPC207613
0.6 Remote Similarity NPC12022
0.6 Remote Similarity NPC275724
0.6 Remote Similarity NPC481914
0.6 Remote Similarity NPC244246
0.6 Remote Similarity NPC278308
0.6 Remote Similarity NPC611247
0.5952 Remote Similarity NPC156840
0.5893 Remote Similarity NPC65935
0.5893 Remote Similarity NPC319282
0.5778 Remote Similarity NPC471693
0.5769 Remote Similarity NPC485986
0.5745 Remote Similarity NPC17943
0.5652 Remote Similarity NPC255675
0.5577 Remote Similarity NPC114298
0.5556 Remote Similarity NPC481913
0.5556 Remote Similarity NPC221049
0.5532 Remote Similarity NPC474320
0.551 Remote Similarity NPC177291
0.551 Remote Similarity NPC127937
0.5472 Remote Similarity NPC4181
0.5472 Remote Similarity NPC201777
0.5472 Remote Similarity NPC604524
0.5435 Remote Similarity NPC165133
0.5435 Remote Similarity NPC242885
0.5435 Remote Similarity NPC95614
0.5435 Remote Similarity NPC232316
0.5333 Remote Similarity NPC257124
0.5312 Remote Similarity NPC52277
0.5294 Remote Similarity NPC51840
0.5294 Remote Similarity NPC82679
0.5283 Remote Similarity NPC212015
0.5273 Remote Similarity NPC164778
0.5273 Remote Similarity NPC163083
0.5227 Remote Similarity NPC91461
0.5227 Remote Similarity NPC7686
0.5227 Remote Similarity NPC40258
0.5217 Remote Similarity NPC140359
0.5217 Remote Similarity NPC474272
0.5208 Remote Similarity NPC85488
0.52 Remote Similarity NPC474214
0.5185 Remote Similarity NPC303680
0.5179 Remote Similarity NPC257976
0.5179 Remote Similarity NPC273686
0.5179 Remote Similarity NPC242372
0.5179 Remote Similarity NPC312404
0.5106 Remote Similarity NPC193544
0.5098 Remote Similarity NPC487676
0.5094 Remote Similarity NPC5018
0.5094 Remote Similarity NPC74817

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC61104 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
0.5333 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