Natural Product: NPC44563

Natural Product IDNPC44563
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
MZIWGWDBQYWPJI-WZRCOZNRSA-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: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 MZIWGWDBQYWPJI-WZRCOZNRSA-N
Standard InCHI InChI=1S/C57H92O26/c1-21(20-73-51-44(69)41(66)37(62)32(17-58)78-51)7-10-30-22(2)35-31(77-30)16-29-27-9-8-25-15-26(11-13-56(25,5)28(27)12-14-57(29,35)6)76-55-50(83-52-45(70)40(65)36(61)23(3)74-52)49(39(64)34(19-60)80-55)82-53-47(72)43(68)48(24(4)75-53)81-54-46(71)42(67)38(63)33(18-59)79-54/h8,21,23-24,26-29,31-55,58-72H,7,9-20H2,1-6H3/t21-,23+,24+,26-,27-,28-,29+,31-,32+,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-/m1/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](CO)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:   1192.59 Volume:   1132.136
?
Van der Waals volume.
Dense:   1.053 LogP:   -0.49
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.42
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.483
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   54.0
TPSA:   404.98
?
Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   15.0 Rings:   10.0
Heavy Atoms:   26.0

MedChem Properties

QED Drug-Likeness Score:   0.064 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.192 Fsp3:   0.93
MCE-18:   193.636
?
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:   0.881 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:   0.348 Promiscuous compounds:   0.107

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.636 MDCK Permeability:   -4.584
Pgp-inhibitor:   0.0 Pgp-substrate:   0.971
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):   0.895
20% Bioavailability (F20%):   0.079 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.006 MRP1:   0.001
Plasma Protein Binding (PPB):   69.015% Volume Distribution (VD):   -0.261
Fu: 18.199%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.001

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:   0.006 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.0
?
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):  -1.102 Half-life (T1/2):  3.787

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.006
Human Hepatotoxicity (H-HT):  0.524 Drug-induced Liver Injury (DILI):  0.986
AMES Toxicity:  0.848 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.008 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.247 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.021 RPMI-8226 Immunitoxicity:  0.639
A549 Cytotoxicity:  0.894 Hek293 Cytotoxicity:  0.107
BCF:   1.535
?
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:   3.563
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.004
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.078
?
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 NPC44563 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
0.8411 Intermediate Similarity NPC308140
0.7182 Intermediate Similarity NPC102016
0.7182 Intermediate Similarity NPC95051
0.6991 Remote Similarity NPC309278
0.6942 Remote Similarity NPC208832
0.687 Remote Similarity NPC218571
0.687 Remote Similarity NPC487615
0.6696 Remote Similarity NPC300557
0.6525 Remote Similarity NPC23808
0.6525 Remote Similarity NPC87998
0.6518 Remote Similarity NPC602423
0.6207 Remote Similarity NPC150057
0.6207 Remote Similarity NPC475182
0.6207 Remote Similarity NPC147753
0.6167 Remote Similarity NPC92710
0.605 Remote Similarity NPC247037
0.6017 Remote Similarity NPC73243
0.6017 Remote Similarity NPC244086
0.6017 Remote Similarity NPC84956
0.6 Remote Similarity NPC128123
0.6 Remote Similarity NPC98696
0.5935 Remote Similarity NPC477811
0.582 Remote Similarity NPC194207
0.582 Remote Similarity NPC22779
0.5785 Remote Similarity NPC269297
0.5785 Remote Similarity NPC222202
0.5772 Remote Similarity NPC249265
0.5766 Remote Similarity NPC486118
0.5714 Remote Similarity NPC48886
0.5714 Remote Similarity NPC475357
0.5714 Remote Similarity NPC94881
0.5615 Remote Similarity NPC477808
0.5591 Remote Similarity NPC232054
0.5583 Remote Similarity NPC6806
0.5565 Remote Similarity NPC254255
0.5537 Remote Similarity NPC480555
0.5537 Remote Similarity NPC150372
0.5528 Remote Similarity NPC486386
0.5517 Remote Similarity NPC306991
0.5517 Remote Similarity NPC94272
0.5462 Remote Similarity NPC248202
0.5462 Remote Similarity NPC486388
0.5424 Remote Similarity NPC113044
0.5424 Remote Similarity NPC283829
0.5424 Remote Similarity NPC161676
0.542 Remote Similarity NPC224314
0.5391 Remote Similarity NPC31896
0.5385 Remote Similarity NPC470432
0.5385 Remote Similarity NPC230507
0.5317 Remote Similarity NPC197003
0.5312 Remote Similarity NPC480553
0.5289 Remote Similarity NPC470433
0.5289 Remote Similarity NPC46190
0.5289 Remote Similarity NPC171073
0.5238 Remote Similarity NPC475333
0.5238 Remote Similarity NPC224098
0.5238 Remote Similarity NPC208383
0.5221 Remote Similarity NPC263359
0.52 Remote Similarity NPC148965
0.5167 Remote Similarity NPC305423
0.5167 Remote Similarity NPC14704
0.5156 Remote Similarity NPC480554
0.5133 Remote Similarity NPC181845
0.5122 Remote Similarity NPC477809
0.5113 Remote Similarity NPC480556
0.5111 Remote Similarity NPC210569
0.5077 Remote Similarity NPC256983
0.5041 Remote Similarity NPC470748
0.5038 Remote Similarity NPC190939

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC44563 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
0.6207 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