Natural Product: NPC94188

Natural Product IDNPC94188
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CMHDLIJKTBWHGX-RQLYAJHYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11126072
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 CMHDLIJKTBWHGX-RQLYAJHYSA-N
Standard InCHI InChI=1S/C59H94O27/c1-22(20-76-53-46(71)43(68)39(64)34(18-60)81-53)8-11-32-23(2)37-33(80-32)17-31-29-10-9-27-16-28(12-14-58(27,6)30(29)13-15-59(31,37)7)79-57-52(86-54-47(72)42(67)38(63)24(3)77-54)51(41(66)36(83-57)21-75-26(5)62)85-55-49(74)45(70)50(25(4)78-55)84-56-48(73)44(69)40(65)35(19-61)82-56/h9,22,24-25,28-31,33-57,60-61,63-74H,8,10-21H2,1-7H3/t22-,24-,25-,28-,29+,30-,31-,33-,34+,35+,36+,37-,38-,39+,40+,41+,42+,43-,44-,45-,46+,47+,48+,49+,50-,51-,52+,53+,54-,55-,56-,57+,58-,59-/m0/s1
SMILES C[C@@H](CCC1=C(C)[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](COC(=O)C)O2)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1234.6 Volume:   1172.882
?
Van der Waals volume.
Dense:   1.053 LogP:   0.268
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.018
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.265
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   19.0 Rigid Bonds:   55.0
TPSA:   411.05
?
Topological Polar Surface Area.
H-Bond Acceptor:   27.0
H-Bond Donor:   14.0 Rings:   10.0
Heavy Atoms:   27.0

MedChem Properties

QED Drug-Likeness Score:   0.049 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.284 Fsp3:   0.915
MCE-18:   194.973
?
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:   0.683 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:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.303 Promiscuous compounds:   0.266

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.967 MDCK Permeability:   -4.862
Pgp-inhibitor:   0.0 Pgp-substrate:   0.998
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):   0.024
20% Bioavailability (F20%):   0.033 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.077
Plasma Protein Binding (PPB):   63.095% Volume Distribution (VD):   -0.362
Fu: 24.989%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.004

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.007 CYP3A4-substrate:   0.943
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.058
?
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):  -0.598 Half-life (T1/2):  3.692

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.457 Drug-induced Liver Injury (DILI):  0.991
AMES Toxicity:  0.992 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.02 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.805 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.025 RPMI-8226 Immunitoxicity:  0.249
A549 Cytotoxicity:  0.925 Hek293 Cytotoxicity:  0.346
BCF:   0.909
?
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:   3.396
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.859
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.841
?
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
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. root n.a. PMID[10230514]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota rhizomes SiMao City, Yunnan Province, China 1996-OCT PMID[11908966]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota Rhizomes n.a. n.a. PMID[12350150]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[12956064]
NPO12186 Oplopanax chironium Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[15104479]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. root n.a. PMID[17611928]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. leaf n.a. PMID[18649321]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. PMID[20715765]
NPO7143 Acacia jacquemontii Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21894904]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25608854]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. PMID[33253561]
NPO1133 Zieria laevigata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12268 Aloe littoralis Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11396 Metzgeria furcata Species Metzgeriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6266 Anzia hypoleucoides Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8399 Psiadia trinervia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14634 Artemisia balchanorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13527 Solanum ecuadorense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3227 Androsace umbellata Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10094 Daphne gnidioides Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13426 Lemmaphyllum microphyllum Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6266 Anzia hypoleucoides Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13332 Tacca chantrieri Species Taccaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12268 Aloe littoralis Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14308 Coleonema pulchrum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14018 Pleurotus salmoneostramineus Species Pleurotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13831 Cephalotaxus oliveri Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9487 Penicillium flexuosum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12093 Papaver orientale Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8399 Psiadia trinervia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1576 Anthriscus sylvestris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7143 Acacia jacquemontii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14634 Artemisia balchanorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11753 Sideroxylon foetidissimum Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5551 Podocarpus sylvestris Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11396 Metzgeria furcata Species Metzgeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1133 Zieria laevigata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11157 Corydalis saxicola Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11909 Othonna arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9126 Stevia maimarensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11585 Geijera salicifolia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10695 Pelargonium zonale Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13723 Salvia eriophora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12186 Oplopanax chironium Species Araliaceae 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 NPC94188 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
0.7895 Intermediate Similarity NPC308140
0.6333 Remote Similarity NPC102016
0.6333 Remote Similarity NPC95051
0.6308 Remote Similarity NPC208832
0.6179 Remote Similarity NPC309278
0.616 Remote Similarity NPC23808
0.616 Remote Similarity NPC87998
0.608 Remote Similarity NPC218571
0.608 Remote Similarity NPC487615
0.5902 Remote Similarity NPC300557
0.5854 Remote Similarity NPC475182
0.5769 Remote Similarity NPC475357
0.5738 Remote Similarity NPC602423
0.5714 Remote Similarity NPC247037
0.568 Remote Similarity NPC73243
0.568 Remote Similarity NPC244086
0.568 Remote Similarity NPC84956
0.5581 Remote Similarity NPC92710
0.5556 Remote Similarity NPC486118
0.5528 Remote Similarity NPC98696
0.5508 Remote Similarity NPC128123
0.5504 Remote Similarity NPC194207
0.5504 Remote Similarity NPC22779
0.5476 Remote Similarity NPC150057
0.5476 Remote Similarity NPC147753
0.5469 Remote Similarity NPC269297
0.5469 Remote Similarity NPC222202
0.5462 Remote Similarity NPC249265
0.5299 Remote Similarity NPC232054
0.5276 Remote Similarity NPC6806
0.5267 Remote Similarity NPC254255
0.5263 Remote Similarity NPC477811
0.5234 Remote Similarity NPC480555
0.5234 Remote Similarity NPC150372
0.5231 Remote Similarity NPC486386
0.5224 Remote Similarity NPC287885
0.5217 Remote Similarity NPC477808
0.5203 Remote Similarity NPC306991
0.5203 Remote Similarity NPC94272
0.5159 Remote Similarity NPC486388
0.5145 Remote Similarity NPC224314
0.5081 Remote Similarity NPC470432
0.5081 Remote Similarity NPC230507
0.5072 Remote Similarity NPC248202
0.5039 Remote Similarity NPC48886
0.5039 Remote Similarity NPC94881

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC94188 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
0.5476 Remote Similarity NPD8450 Suspended

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