Natural Product: NPC269632

Natural Product IDNPC269632
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DPQYOKVMVCQHMY-MLGYPOCJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 6428433
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids

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 DPQYOKVMVCQHMY-MLGYPOCJSA-N
Standard InCHI InChI=1S/C15H26O/c1-11(2)12-6-9-14(3)7-5-8-15(4,16)13(14)10-12/h12-13,16H,1,5-10H2,2-4H3/t12?,13?,14?,15-/m1/s1
SMILES C=C(C)C1CCC2(C)CCC[C@](C)(C2C1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   222.2 Volume:   257.037
?
Van der Waals volume.
Dense:   0.864 LogP:   3.339
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.262
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.911
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   12.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.667 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.095 Fsp3:   0.867
MCE-18:   40.714
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.018 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.011
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.856 Promiscuous compounds:   0.139

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.723 MDCK Permeability:   -4.861
Pgp-inhibitor:   0.385 Pgp-substrate:   0.002
PAMPA:   0.034
?
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%):   0.003 30% Bioavailability (F30%):   0.006
50% Bioavailability (F50%):   0.376

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.832 MRP1:   0.884
Plasma Protein Binding (PPB):   95.544% Volume Distribution (VD):   0.321
Fu: 4.854%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.731
OATP1B3 inhibitor:   0.782 BCRP inhibitor:   0.563
BSEP inhibitor:   0.982

ADMET: Metabolism

CYP1A2-inhibitor:   0.692 CYP1A2-substrate:   0.049
CYP2C19-inhibitor:   0.862 CYP2C19-substrate:   0.026
CYP2C9-inhibitor:   0.491 CYP2C9-substrate:   0.003
CYP2D6-inhibitor:   0.551 CYP2D6-substrate:   0.047
CYP3A4-inhibitor:   0.032 CYP3A4-substrate:   0.395
CYP2B6-substrate:   0.29 CYP2C8-inhibitor:   0.897
HLM stability:   0.417
?
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):  15.966 Half-life (T1/2):  1.345

ADMET: Toxicity

hERG Blockers:  0.055 hERG Blockers (10um):  0.368
Human Hepatotoxicity (H-HT):  0.559 Drug-induced Liver Injury (DILI):  0.049
AMES Toxicity:  0.068 Rat Oral Acute Toxicity:  0.092
Maximum Recommended Daily Dose:  0.503 Skin Sensitization:  0.833
Carcinogencity:  0.709 Eye Corrosion:  0.917
Eye Irritation:  0.992 Respiratory Toxicity:  0.495
Drug-induced Neurotoxicity:  0.169 Ototoxicity:  0.527
Hematotoxicity:  0.196 Drug-induced Nephrotoxicity:  0.215
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.033
A549 Cytotoxicity:  0.037 Hek293 Cytotoxicity:  0.089
BCF:   2.07
?
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:   3.81
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.232
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.564
?
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
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. leaf n.a. DOI[10.1016/j.foodchem.2010.03.088]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[10364842]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[12392098]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. rhizome n.a. PMID[21563811]
NPO25682 Acorus calamus Species Acoraceae Eukaryota rhizomes n.a. n.a. PMID[22671987]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[23373216]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[24996657]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. root n.a. PMID[25767328]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[31401871]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[31738062]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[34486118]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[35344272]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. PMID[35872238]
NPO44665 Achillea coarctata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36006860]
NPO14951 Zanthoxylum acanthopodium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[36014481]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[36558111]
NPO47617 Echinops polyceras Genus Asteraceae Eukaryota n.a. n.a. n.a. PMID[37241978]
NPO14951 Zanthoxylum acanthopodium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[37471031]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37571040]
NPO64248 Eucalyptus patellaris Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37894690]
NPO55150 Grewia bulot Genus Malvaceae Eukaryota n.a. n.a. n.a. PMID[37910669]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37917799]
NPO58210 Anthemis palestina Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38005810]
NPO57072 Prangos trifida Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[38247600]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38677581]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39064968]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[4013523]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14951 Zanthoxylum acanthopodium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44665 Achillea coarctata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO14951 Zanthoxylum acanthopodium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO14951 Zanthoxylum acanthopodium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25682 Acorus calamus Species Acoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17755 Inula helenium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3359 Psidium guajava Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14951 Zanthoxylum acanthopodium 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
NPO14951 Zanthoxylum acanthopodium Oil Leaves n.a. n.a. % PMID[37471031]
NPO14951 Zanthoxylum acanthopodium Oil Stems 0.5 n.a. n.a. % PMID[37471031]
NPO3359 Psidium guajava Oil Leaves 6.35 n.a. n.a. % PMID[36558111]
NPO3359 Psidium guajava Oil n.a. 5.79±0.16 n.a. n.a. % PMID[37917799]
NPO44665 Achillea coarctata Oil n.a. 0.5 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 0.6 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 0.2 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 0.7 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 2.2 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 0.9 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 0.4 n.a. n.a. % PMID[36006860]
NPO47617 Echinops polyceras Hydro distillation Inflorescences 0.17 n.a. n.a. % PMID[37241978]
NPO55150 Grewia bulot Oil Leaves 4.0 n.a. n.a. % PMID[37910669]
NPO57072 Prangos trifida Oil Fruits 0.2 n.a. n.a. % PMID[38247600]
NPO57072 Prangos trifida Oil Roots 0.9 n.a. n.a. % PMID[38247600]
NPO58210 Anthemis palestina Sun-dried n.a. 0.93 n.a. n.a. % PMID[38005810]
NPO58210 Anthemis palestina Oven-dried n.a. 0.23 n.a. n.a. % PMID[38005810]
NPO58210 Anthemis palestina Oil n.a. 0.19 n.a. n.a. % PMID[38005810]
NPO64248 Eucalyptus patellaris Oil n.a. 0.3 n.a. n.a. % PMID[37894690]

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 NPC269632 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 NPC189290
1.0 High Similarity NPC474769
0.8 Intermediate Similarity NPC258595
0.7568 Intermediate Similarity NPC605486
0.6829 Remote Similarity NPC263951
0.6571 Remote Similarity NPC36002
0.6571 Remote Similarity NPC102336
0.5581 Remote Similarity NPC39362
0.5581 Remote Similarity NPC602335
0.55 Remote Similarity NPC185874
0.55 Remote Similarity NPC139207

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC269632 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