Natural Product: NPC265644

Natural Product IDNPC265644
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IQDXAJNQKSIPGB-PRFTWSQHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11335274
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001357] Acyclic diterpenoids

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 IQDXAJNQKSIPGB-PRFTWSQHSA-N
Standard InCHI InChI=1S/C20H34O/c1-7-20(6,21)16-10-15-19(5)14-9-13-18(4)12-8-11-17(2)3/h7,11,13,15,21H,1,8-10,12,14,16H2,2-6H3/b18-13+,19-15+/t20-/m0/s1
SMILES C=C[C@@](C)(CC/C=C(C)/CC/C=C(C)/CCC=C(C)C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   290.26 Volume:   352.721
?
Van der Waals volume.
Dense:   0.823 LogP:   6.048
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.978
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.077
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   4.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.48 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.536 Fsp3:   0.6
MCE-18:   6.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.334 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.989 Promiscuous compounds:   0.259

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.558 MDCK Permeability:   -4.756
Pgp-inhibitor:   0.999 Pgp-substrate:   0.0
PAMPA:   0.004
?
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):   0.014
20% Bioavailability (F20%):   0.153 30% Bioavailability (F30%):   0.185
50% Bioavailability (F50%):   0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.946
Plasma Protein Binding (PPB):   88.646% Volume Distribution (VD):   -0.212
Fu: 8.738%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.009
BSEP inhibitor:   0.99

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.886
CYP2C19-inhibitor:   0.957 CYP2C19-substrate:   0.027
CYP2C9-inhibitor:   0.548 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.89 CYP2D6-substrate:   0.728
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.484
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.896
HLM stability:   0.999
?
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):  10.346 Half-life (T1/2):  0.988

ADMET: Toxicity

hERG Blockers:  0.059 hERG Blockers (10um):  0.478
Human Hepatotoxicity (H-HT):  0.684 Drug-induced Liver Injury (DILI):  0.024
AMES Toxicity:  0.062 Rat Oral Acute Toxicity:  0.184
Maximum Recommended Daily Dose:  0.323 Skin Sensitization:  0.988
Carcinogencity:  0.352 Eye Corrosion:  0.464
Eye Irritation:  0.977 Respiratory Toxicity:  0.985
Drug-induced Neurotoxicity:  0.562 Ototoxicity:  0.286
Hematotoxicity:  0.163 Drug-induced Nephrotoxicity:  0.351
Genotoxicity:  0.093 RPMI-8226 Immunitoxicity:  0.065
A549 Cytotoxicity:  0.384 Hek293 Cytotoxicity:  0.21
BCF:   2.268
?
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:   5.018
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.566
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.501
?
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]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(99)00119-3]
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]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[37049761]
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]
NPO11971 Laurencia microcladia Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20553 Zingiber officinale Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27288 Citrus maxima Species Rutaceae 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]
NPO27288 Citrus maxima Species Rutaceae 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]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO27288 Citrus maxima Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO27288 Citrus maxima Species Rutaceae 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]
NPO11971 Laurencia microcladia Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27288 Citrus maxima Species Rutaceae 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 NPC265644 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 NPC67761
1.0 High Similarity NPC209279
1.0 High Similarity NPC194586
1.0 High Similarity NPC108494
1.0 High Similarity NPC51758
0.76 Intermediate Similarity NPC68889
0.76 Intermediate Similarity NPC180871
0.7037 Intermediate Similarity NPC88079
0.6562 Remote Similarity NPC227135
0.5769 Remote Similarity NPC123965
0.5769 Remote Similarity NPC115959
0.5667 Remote Similarity NPC29091
0.5667 Remote Similarity NPC103213
0.5667 Remote Similarity NPC300623
0.5667 Remote Similarity NPC213538
0.5667 Remote Similarity NPC269823
0.5667 Remote Similarity NPC39222
0.5667 Remote Similarity NPC9860
0.5294 Remote Similarity NPC140501

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC265644 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
0.5294 Remote Similarity NPD4265 Phase 2

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