Natural Product: NPC71375

Natural Product IDNPC71375
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PSOQPSXOOXHHBU-NJAOXFEXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002724] Steroidal alkaloids
          • [CHEMONTID:0002731] Conanine-type alkaloids

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 PSOQPSXOOXHHBU-NJAOXFEXSA-N
Standard InCHI InChI=1S/C22H31NO/c1-14-18-6-7-20-17-5-4-15-12-16(24)8-10-21(15,2)19(17)9-11-22(18,20)13-23(14)3/h8,10,12,14,17-20H,4-7,9,11,13H2,1-3H3/t14-,17+,18+,19-,20+,21-,22+/m0/s1
SMILES C[C@H]1[C@H]2CC[C@@H]3[C@@H]4CCC5=CC(=O)C=C[C@]5(C)[C@H]4CC[C@@]23CN1C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   325.24 Volume:   358.163
?
Van der Waals volume.
Dense:   0.908 LogP:   2.608
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.73
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.272
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   25.0
TPSA:   20.31
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   5.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.664 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.893 Fsp3:   0.773
MCE-18:   107.821
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.841 Fluc inhibitor:   0.078
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.115
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.061 Promiscuous compounds:   0.32

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.986 MDCK Permeability:   -4.643
Pgp-inhibitor:   0.508 Pgp-substrate:   0.022
PAMPA:   0.007
?
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%):   0.176 30% Bioavailability (F30%):   0.592
50% Bioavailability (F50%):   0.906

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.984 MRP1:   0.667
Plasma Protein Binding (PPB):   78.449% Volume Distribution (VD):   0.667
Fu: 20.881%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.293
OATP1B3 inhibitor:   0.192 BCRP inhibitor:   0.036
BSEP inhibitor:   0.911

ADMET: Metabolism

CYP1A2-inhibitor:   0.999 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.999 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.021 CYP2C9-substrate:   0.007
CYP2D6-inhibitor:   0.743 CYP2D6-substrate:   0.008
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.968
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.004
HLM stability:   0.107
?
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):  12.835 Half-life (T1/2):  1.589

ADMET: Toxicity

hERG Blockers:  0.221 hERG Blockers (10um):  0.406
Human Hepatotoxicity (H-HT):  0.673 Drug-induced Liver Injury (DILI):  0.109
AMES Toxicity:  0.353 Rat Oral Acute Toxicity:  0.709
Maximum Recommended Daily Dose:  0.901 Skin Sensitization:  0.889
Carcinogencity:  0.848 Eye Corrosion:  0.104
Eye Irritation:  0.898 Respiratory Toxicity:  0.95
Drug-induced Neurotoxicity:  0.452 Ototoxicity:  0.43
Hematotoxicity:  0.271 Drug-induced Nephrotoxicity:  0.384
Genotoxicity:  0.921 RPMI-8226 Immunitoxicity:  0.102
A549 Cytotoxicity:  0.058 Hek293 Cytotoxicity:  0.451
BCF:   1.931
?
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:   3.93
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.988
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.677
?
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
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. seed n.a. DOI[10.1007/s11418-005-0009-z]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[11251292]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota stem bark n.a. n.a. PMID[17489632]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. stem n.a. PMID[18484536]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota stem bark Mukono, Uganda 2005-JUN PMID[19008110]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19836230]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20337486]
NPO2713 Xylopia caudata Species Annonaceae Eukaryota Trunk bark the dense rainy forest of Jelebu, in Negeri Sembilan state, Malaysia 2006-FEB PMID[20481544]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21116437]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22026385]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[31125231]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[6875511]
NPO2713 Xylopia caudata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8526 Erythrina abyssinica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9530 Scrophularia nodosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27885 Aspergillus nidulans Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO522 Oenanthe javanica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2713 Xylopia caudata Species Annonaceae 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 NPC71375 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
0.569 Remote Similarity NPC92327
0.5333 Remote Similarity NPC54123
0.5323 Remote Similarity NPC6434
0.5312 Remote Similarity NPC105197
0.5156 Remote Similarity NPC176107

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC71375 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
0.5323 Remote Similarity NPD4195 Phase 4

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