Natural Product: NPC122470

Natural Product IDNPC122470
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 HTVILJWNNLIWMP-IJDPAOOOSA-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:0003569] Pregnane steroids
          • [CHEMONTID:0001468] Gluco/mineralocorticoids, progestogins and derivatives

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 HTVILJWNNLIWMP-IJDPAOOOSA-N
Standard InCHI InChI=1S/C22H35NO/c1-14(23-4)18-7-8-19-17-6-5-15-13-16(24)9-11-21(15,2)20(17)10-12-22(18,19)3/h13-14,17-20,23H,5-12H2,1-4H3/t14-,17-,18+,19-,20-,21-,22+/m0/s1
SMILES C[C@@H]([C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C)NC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   329.27 Volume:   369.356
?
Van der Waals volume.
Dense:   0.891 LogP:   3.721
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.388
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.426
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   21.0
TPSA:   29.1
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.792 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.187 Fsp3:   0.864
MCE-18:   67.073
?
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:   0.595 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.01
?
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:   0.025 Promiscuous compounds:   0.597

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.094 MDCK Permeability:   -4.848
Pgp-inhibitor:   0.003 Pgp-substrate:   0.011
PAMPA:   0.006
?
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%):   0.0 30% Bioavailability (F30%):   0.048
50% Bioavailability (F50%):   0.767

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.629 MRP1:   0.027
Plasma Protein Binding (PPB):   79.2% Volume Distribution (VD):   0.166
Fu: 18.353%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.027
BSEP inhibitor:   0.026

ADMET: Metabolism

CYP1A2-inhibitor:   0.996 CYP1A2-substrate:   0.009
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.994
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.253
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.046
?
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):  15.463 Half-life (T1/2):  0.875

ADMET: Toxicity

hERG Blockers:  0.393 hERG Blockers (10um):  0.623
Human Hepatotoxicity (H-HT):  0.851 Drug-induced Liver Injury (DILI):  0.021
AMES Toxicity:  0.049 Rat Oral Acute Toxicity:  0.227
Maximum Recommended Daily Dose:  0.79 Skin Sensitization:  0.822
Carcinogencity:  0.364 Eye Corrosion:  0.104
Eye Irritation:  0.519 Respiratory Toxicity:  0.888
Drug-induced Neurotoxicity:  0.426 Ototoxicity:  0.761
Hematotoxicity:  0.628 Drug-induced Nephrotoxicity:  0.452
Genotoxicity:  0.913 RPMI-8226 Immunitoxicity:  0.026
A549 Cytotoxicity:  0.088 Hek293 Cytotoxicity:  0.437
BCF:   0.988
?
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:   3.514
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.046
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.432
?
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 NPC122470 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
0.6863 Remote Similarity NPC307176
0.6863 Remote Similarity NPC321874
0.6792 Remote Similarity NPC282593
0.6667 Remote Similarity NPC159577
0.6481 Remote Similarity NPC214043
0.6481 Remote Similarity NPC85774
0.6364 Remote Similarity NPC35734
0.6364 Remote Similarity NPC115023
0.6364 Remote Similarity NPC602429
0.625 Remote Similarity NPC149203
0.625 Remote Similarity NPC237712
0.614 Remote Similarity NPC249312
0.5902 Remote Similarity NPC320514
0.5741 Remote Similarity NPC139397
0.5536 Remote Similarity NPC2634
0.5536 Remote Similarity NPC265782
0.5536 Remote Similarity NPC251929
0.5345 Remote Similarity NPC227064
0.5345 Remote Similarity NPC329043
0.5345 Remote Similarity NPC58841
0.5345 Remote Similarity NPC161423
0.5333 Remote Similarity NPC323765
0.5254 Remote Similarity NPC144258
0.5254 Remote Similarity NPC327115
0.5224 Remote Similarity NPC187159
0.5082 Remote Similarity NPC303613

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC122470 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
0.6863 Remote Similarity NPD4747 Phase 4
0.5932 Remote Similarity NPD5737 Phase 4
0.5738 Remote Similarity NPD6672 Phase 4
0.5536 Remote Similarity NPD4691 Approved
0.5345 Remote Similarity NPD3666 Phase 4
0.5345 Remote Similarity NPD4221 Phase 4
0.5246 Remote Similarity NPD5330 Phase 4
0.5082 Remote Similarity NPD4693 Phase 3
0.5079 Remote Similarity NPD6409 Approved

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