Natural Product: NPC206386

Natural Product IDNPC206386
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
OGBIFUPQNPPQBB-OQDUZEMASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968854
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 OGBIFUPQNPPQBB-OQDUZEMASA-N
Standard InCHI InChI=1S/C49H80O22/c1-19-7-12-49(63-17-19)20(2)30-26(71-49)14-25-23-6-5-21-13-22(8-10-47(21,3)24(23)9-11-48(25,30)4)64-46-41(36(57)32(53)28(16-51)66-46)68-42-37(58)33(54)29(18-62-42)67-44-39(60)35(56)40(61)45(70-44)69-43-38(59)34(55)31(52)27(15-50)65-43/h19-46,50-61H,5-18H2,1-4H3/t19?,20?,21?,22?,23?,24?,25?,26?,27-,28-,29+,30?,31-,32-,33+,34+,35+,36+,37-,38-,39-,40+,41-,42+,43+,44-,45-,46-,47?,48?,49?/m1/s1
SMILES CC1CCC2(C(C)C3C(CC4C5CCC6CC(CCC6(C)C5CCC34C)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O[C@H]3[C@@H]([C@H]([C@H](CO3)O[C@H]3[C@@H]([C@@H]([C@@H]([C@H](O[C@H]4[C@@H]([C@H]([C@@H]([C@@H](CO)O4)O)O)O)O3)O)O)O)O)O)O2)OC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1020.51 Volume:   963.88
?
Van der Waals volume.
Dense:   1.059 LogP:   0.764
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.446
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.522
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   54.0
TPSA:   335.06
?
Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   12.0 Rings:   10.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.102 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.119 Fsp3:   1.0
MCE-18:   259.796
?
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:   0.556 Fluc inhibitor:   0.213
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.013
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.029
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.333 Promiscuous compounds:   0.007

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.41 MDCK Permeability:   -4.949
Pgp-inhibitor:   0.0 Pgp-substrate:   0.059
PAMPA:   0.989
?
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):   0.275
20% Bioavailability (F20%):   0.001 30% Bioavailability (F30%):   0.962
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.96
Plasma Protein Binding (PPB):   58.335% Volume Distribution (VD):   -0.402
Fu: 29.276%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.901
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.0
BSEP inhibitor:   0.005

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.014 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.001
HLM stability:   0.037
?
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):  -0.367 Half-life (T1/2):  4.413

ADMET: Toxicity

hERG Blockers:  0.019 hERG Blockers (10um):  0.075
Human Hepatotoxicity (H-HT):  0.721 Drug-induced Liver Injury (DILI):  0.761
AMES Toxicity:  0.927 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.013 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  1.0
Hematotoxicity:  0.182 Drug-induced Nephrotoxicity:  0.406
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.239
A549 Cytotoxicity:  0.872 Hek293 Cytotoxicity:  0.74
BCF:   1.867
?
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:   3.944
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.246
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.414
?
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
NPO25434 Asparagus adscendens Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25434 Asparagus adscendens Species Asparagaceae 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 NPC206386 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
0.8539 High Similarity NPC211354
0.8391 Intermediate Similarity NPC297348
0.8391 Intermediate Similarity NPC249204
0.8391 Intermediate Similarity NPC48339
0.8391 Intermediate Similarity NPC141769
0.8391 Intermediate Similarity NPC477547
0.8 Intermediate Similarity NPC477451
0.7766 Intermediate Similarity NPC107962
0.7526 Intermediate Similarity NPC160426
0.7188 Intermediate Similarity NPC107188
0.7087 Intermediate Similarity NPC128572
0.697 Remote Similarity NPC6295
0.6947 Remote Similarity NPC294686
0.6907 Remote Similarity NPC206003
0.6907 Remote Similarity NPC473610
0.6842 Remote Similarity NPC325828
0.6842 Remote Similarity NPC177834
0.6822 Remote Similarity NPC475625
0.6796 Remote Similarity NPC475643
0.6771 Remote Similarity NPC234352
0.6765 Remote Similarity NPC475351
0.6667 Remote Similarity NPC19400
0.6633 Remote Similarity NPC222731
0.6571 Remote Similarity NPC92890
0.6505 Remote Similarity NPC113044
0.6505 Remote Similarity NPC283829
0.6505 Remote Similarity NPC161676
0.6389 Remote Similarity NPC97700
0.6389 Remote Similarity NPC30856
0.63 Remote Similarity NPC250393
0.6263 Remote Similarity NPC291203
0.6263 Remote Similarity NPC217205
0.6262 Remote Similarity NPC477809
0.6239 Remote Similarity NPC184617
0.6204 Remote Similarity NPC471464
0.6195 Remote Similarity NPC83137
0.6176 Remote Similarity NPC54619
0.6154 Remote Similarity NPC125324
0.614 Remote Similarity NPC132080
0.6139 Remote Similarity NPC474399
0.6095 Remote Similarity NPC141433
0.6055 Remote Similarity NPC51172
0.6055 Remote Similarity NPC49032
0.596 Remote Similarity NPC485594
0.5922 Remote Similarity NPC128123
0.5877 Remote Similarity NPC232037
0.5849 Remote Similarity NPC485595
0.5826 Remote Similarity NPC470864
0.581 Remote Similarity NPC264101
0.5794 Remote Similarity NPC195297
0.5789 Remote Similarity NPC116756
0.5755 Remote Similarity NPC215408
0.5752 Remote Similarity NPC475319
0.5743 Remote Similarity NPC181845
0.5714 Remote Similarity NPC480555
0.5714 Remote Similarity NPC150372
0.5636 Remote Similarity NPC473601
0.56 Remote Similarity NPC24960
0.5583 Remote Similarity NPC470866
0.5487 Remote Similarity NPC300557
0.5478 Remote Similarity NPC115165
0.5462 Remote Similarity NPC233433
0.5462 Remote Similarity NPC480553
0.5446 Remote Similarity NPC470433
0.5446 Remote Similarity NPC46190
0.5446 Remote Similarity NPC171073
0.5421 Remote Similarity NPC306131
0.5421 Remote Similarity NPC200802
0.5385 Remote Similarity NPC475333
0.5385 Remote Similarity NPC224098
0.5385 Remote Similarity NPC208383
0.5373 Remote Similarity NPC481189
0.5339 Remote Similarity NPC194207
0.5339 Remote Similarity NPC22779
0.5321 Remote Similarity NPC485601
0.531 Remote Similarity NPC602423
0.5308 Remote Similarity NPC481190
0.53 Remote Similarity NPC277715
0.5299 Remote Similarity NPC269297
0.5299 Remote Similarity NPC222202
0.5294 Remote Similarity NPC480554
0.528 Remote Similarity NPC220836
0.5263 Remote Similarity NPC329807
0.5242 Remote Similarity NPC480556
0.5221 Remote Similarity NPC329727
0.5221 Remote Similarity NPC202898
0.5179 Remote Similarity NPC305423
0.5179 Remote Similarity NPC14704
0.5167 Remote Similarity NPC108072
0.5135 Remote Similarity NPC470432
0.5135 Remote Similarity NPC230507
0.5126 Remote Similarity NPC13193
0.5126 Remote Similarity NPC309278
0.5124 Remote Similarity NPC476112
0.5124 Remote Similarity NPC307534
0.5122 Remote Similarity NPC232054
0.5089 Remote Similarity NPC70204
0.5086 Remote Similarity NPC6806
0.5049 Remote Similarity NPC473774
0.5049 Remote Similarity NPC481419
0.5049 Remote Similarity NPC481417
0.5043 Remote Similarity NPC151134
0.5042 Remote Similarity NPC475550
0.504 Remote Similarity NPC94086
0.504 Remote Similarity NPC473817
0.5039 Remote Similarity NPC477808
0.5038 Remote Similarity NPC330026

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC206386 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
0.6842 Remote Similarity NPD8171 Phase 2
0.5849 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