Natural Product: NPC95103

Natural Product IDNPC95103
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ANQIEVFGUHZDQN-WQXHJAQXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101693300
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal saponins

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 ANQIEVFGUHZDQN-WQXHJAQXSA-N
Standard InCHI InChI=1S/C55H88O27/c1-21-7-10-55(73-17-21)22(2)34-28(82-55)12-27-25-6-5-23-11-24(8-9-52(23,3)26(25)13-33(60)53(27,34)4)74-48-42(68)39(65)43(31(16-58)77-48)79-50-45(81-49-41(67)38(64)35(61)29(14-56)75-49)44(37(63)30(15-57)76-50)80-47-40(66)36(62)32(18-71-47)78-51-46(69)54(70,19-59)20-72-51/h21-32,34-51,56-59,61-70H,5-20H2,1-4H3/t21-,22+,23+,24+,25-,26+,27+,28+,29-,30-,31-,32-,34+,35-,36+,37-,38+,39-,40-,41-,42-,43+,44+,45-,46+,47+,48-,49+,50+,51+,52+,53-,54-,55-/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC[C@H]6C[C@H](CC[C@]6(C)[C@H]5CC(=O)[C@]34C)O[C@H]3[C@@H]([C@H]([C@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O[C@H]3[C@@H]([C@H]([C@@H](CO3)O[C@H]3[C@@H]([C@@](CO)(CO3)O)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)O)O2)OC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1180.55 Volume:   1100.414
?
Van der Waals volume.
Dense:   1.073 LogP:   0.185
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.982
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.183
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   60.0
TPSA:   411.05
?
Topological Polar Surface Area.
H-Bond Acceptor:   27.0
H-Bond Donor:   14.0 Rings:   11.0
Heavy Atoms:   27.0

MedChem Properties

QED Drug-Likeness Score:   0.073 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.709 Fsp3:   0.982
MCE-18:   292.147
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.566 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
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:   0.376 Promiscuous compounds:   0.54

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.854 MDCK Permeability:   -5.066
Pgp-inhibitor:   0.0 Pgp-substrate:   0.96
PAMPA:   1.0
?
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):   0.977
20% Bioavailability (F20%):   0.769 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.01
Plasma Protein Binding (PPB):   37.785% Volume Distribution (VD):   -0.47
Fu: 52.385%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.081
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.015 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.681
HLM stability:   0.003
?
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):  -0.229 Half-life (T1/2):  3.113

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.851 Drug-induced Liver Injury (DILI):  0.999
AMES Toxicity:  0.999 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.003 Skin Sensitization:  1.0
Carcinogencity:  0.223 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.73 Drug-induced Nephrotoxicity:  0.975
Genotoxicity:  0.028 RPMI-8226 Immunitoxicity:  0.499
A549 Cytotoxicity:  0.999 Hek293 Cytotoxicity:  0.989
BCF:   1.026
?
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:   3.291
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.539
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.623
?
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
NPO27348 Wyethia glabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27348 Wyethia glabra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27583 Senecio uspallatensis Species Asteraceae 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 NPC95103 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
0.8393 Intermediate Similarity NPC233433
0.8051 Intermediate Similarity NPC220836
0.7797 Intermediate Similarity NPC94086
0.7797 Intermediate Similarity NPC473817
0.7699 Intermediate Similarity NPC475319
0.7345 Intermediate Similarity NPC92890
0.7155 Intermediate Similarity NPC97700
0.7155 Intermediate Similarity NPC30856
0.7 Intermediate Similarity NPC108072
0.6885 Remote Similarity NPC132080
0.6864 Remote Similarity NPC184617
0.6692 Remote Similarity NPC305771
0.6692 Remote Similarity NPC94072
0.6692 Remote Similarity NPC169816
0.6667 Remote Similarity NPC83137
0.6639 Remote Similarity NPC232037
0.6613 Remote Similarity NPC92297
0.6579 Remote Similarity NPC215408
0.6557 Remote Similarity NPC116756
0.6496 Remote Similarity NPC475351
0.6462 Remote Similarity NPC15918
0.646 Remote Similarity NPC206003
0.646 Remote Similarity NPC473610
0.6452 Remote Similarity NPC470864
0.6441 Remote Similarity NPC202898
0.6385 Remote Similarity NPC273002
0.6328 Remote Similarity NPC470866
0.625 Remote Similarity NPC325828
0.6154 Remote Similarity NPC107962
0.6129 Remote Similarity NPC115165
0.5983 Remote Similarity NPC107188
0.5948 Remote Similarity NPC250393
0.594 Remote Similarity NPC473505
0.5906 Remote Similarity NPC475625
0.5891 Remote Similarity NPC476112
0.5891 Remote Similarity NPC307534
0.5887 Remote Similarity NPC51172
0.5887 Remote Similarity NPC49032
0.5846 Remote Similarity NPC477811
0.5833 Remote Similarity NPC125324
0.5833 Remote Similarity NPC481189
0.5786 Remote Similarity NPC481190
0.576 Remote Similarity NPC249553
0.5734 Remote Similarity NPC329807
0.5714 Remote Similarity NPC211354
0.5685 Remote Similarity NPC329727
0.5682 Remote Similarity NPC31896
0.5669 Remote Similarity NPC98018
0.5669 Remote Similarity NPC284104
0.5669 Remote Similarity NPC103616
0.5659 Remote Similarity NPC473518
0.5645 Remote Similarity NPC473601
0.5634 Remote Similarity NPC330026
0.5615 Remote Similarity NPC232611
0.561 Remote Similarity NPC160426
0.5581 Remote Similarity NPC470863
0.553 Remote Similarity NPC470862
0.5508 Remote Similarity NPC234352
0.5507 Remote Similarity NPC210569
0.5489 Remote Similarity NPC84111
0.5489 Remote Similarity NPC287483
0.5489 Remote Similarity NPC470865
0.5474 Remote Similarity NPC477807
0.5469 Remote Similarity NPC128572
0.5447 Remote Similarity NPC6295
0.5424 Remote Similarity NPC297348
0.5424 Remote Similarity NPC249204
0.5424 Remote Similarity NPC48339
0.5424 Remote Similarity NPC177834
0.5424 Remote Similarity NPC141769
0.5424 Remote Similarity NPC477547
0.5391 Remote Similarity NPC300557
0.5271 Remote Similarity NPC182900
0.5235 Remote Similarity NPC329820
0.5234 Remote Similarity NPC602423
0.5214 Remote Similarity NPC477808
0.5207 Remote Similarity NPC477451
0.5203 Remote Similarity NPC19400
0.5194 Remote Similarity NPC477809
0.5145 Remote Similarity NPC470867
0.5145 Remote Similarity NPC262050
0.5116 Remote Similarity NPC475643
0.5115 Remote Similarity NPC151134
0.5075 Remote Similarity NPC309278
0.5069 Remote Similarity NPC263359

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC95103 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
0.625 Remote Similarity NPD8171 Phase 2
0.5966 Remote Similarity NPD8170 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