Natural Product: NPC256909

Natural Product IDNPC256909
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
XFQHPZLNJGZIIH-DELHDUSRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 3081325
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 XFQHPZLNJGZIIH-DELHDUSRSA-N
Standard InCHI InChI=1S/C59H96O26/c1-24-34(63)38(67)42(71)48(77-24)84-46-41(70)35(64)25(2)78-52(46)85-47-45(83-50-44(73)40(69)37(66)29(21-61)80-50)30(81-49-43(72)39(68)36(65)28(20-60)79-49)22-76-51(47)82-33-12-13-55(5)31(56(33,6)23-62)11-14-58(8)32(55)10-9-26-27-19-54(3,4)15-17-59(27,53(74)75)18-16-57(26,58)7/h9,24-25,27-52,60-73H,10-23H2,1-8H3,(H,74,75)/t24-,25-,27+,28+,29+,30-,31?,32+,33-,34-,35-,36+,37+,38+,39-,40-,41+,42+,43+,44+,45-,46+,47+,48-,49-,50+,51-,52-,55-,56?,57+,58+,59-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H]([C@H]([C@H](C)O[C@H]1O[C@@H]1[C@H]([C@H](CO[C@H]1O[C@H]1CC[C@@]2(C)C(CC[C@]3(C)[C@@H]2CC=C2[C@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O)C1(C)CO)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1220.62 Volume:   1166.728
?
Van der Waals volume.
Dense:   1.046 LogP:   -0.231
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.908
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.075
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   57.0
TPSA:   412.82
?
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:   0.066 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.251 Fsp3:   0.949
MCE-18:   217.043
?
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:   0.786 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.347 Promiscuous compounds:   0.132

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.05 MDCK Permeability:   -5.123
Pgp-inhibitor:   0.0 Pgp-substrate:   0.695
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):   0.182
20% Bioavailability (F20%):   0.023 30% Bioavailability (F30%):   0.951
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.233
Plasma Protein Binding (PPB):   66.518% Volume Distribution (VD):   -0.308
Fu: 20.901%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

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:   0.001 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.099
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):  -0.856 Half-life (T1/2):  4.938

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.677 Drug-induced Liver Injury (DILI):  0.98
AMES Toxicity:  0.903 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.48 Drug-induced Nephrotoxicity:  0.992
Genotoxicity:  0.042 RPMI-8226 Immunitoxicity:  0.241
A549 Cytotoxicity:  0.573 Hek293 Cytotoxicity:  0.205
BCF:   0.977
?
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:   3.46
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.949
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.887
?
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
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8516 Dipsacus asperoides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8516 Dipsacus asperoides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8516 Dipsacus asperoides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8516 Dipsacus asperoides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8516 Dipsacus asperoides Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10861 Dipsacus asper Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8516 Dipsacus asperoides Species Caprifoliaceae 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 NPC256909 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
0.8137 Intermediate Similarity NPC139044
0.8061 Intermediate Similarity NPC12288
0.7624 Intermediate Similarity NPC174679
0.7624 Intermediate Similarity NPC279554
0.7624 Intermediate Similarity NPC59804
0.7547 Intermediate Similarity NPC257468
0.7453 Intermediate Similarity NPC471383
0.7451 Intermediate Similarity NPC25605
0.7339 Intermediate Similarity NPC323359
0.7248 Intermediate Similarity NPC276093
0.7157 Intermediate Similarity NPC164194
0.7113 Intermediate Similarity NPC204407
0.7048 Intermediate Similarity NPC127056
0.7043 Intermediate Similarity NPC323341
0.7019 Intermediate Similarity NPC136877
0.6952 Remote Similarity NPC56713
0.6789 Remote Similarity NPC114304
0.6752 Remote Similarity NPC133818
0.6726 Remote Similarity NPC324875
0.6726 Remote Similarity NPC292677
0.6667 Remote Similarity NPC488564
0.6667 Remote Similarity NPC270667
0.6667 Remote Similarity NPC472949
0.6667 Remote Similarity NPC488561
0.6585 Remote Similarity NPC471385
0.6555 Remote Similarity NPC166422
0.6538 Remote Similarity NPC473538
0.6535 Remote Similarity NPC606107
0.6446 Remote Similarity NPC54636
0.6417 Remote Similarity NPC219180
0.6306 Remote Similarity NPC22956
0.6281 Remote Similarity NPC251263
0.6273 Remote Similarity NPC109079
0.6218 Remote Similarity NPC476992
0.6214 Remote Similarity NPC28198
0.6214 Remote Similarity NPC476123
0.614 Remote Similarity NPC104400
0.614 Remote Similarity NPC10320
0.6134 Remote Similarity NPC62725
0.6121 Remote Similarity NPC79718
0.6121 Remote Similarity NPC119794
0.6106 Remote Similarity NPC469945
0.6075 Remote Similarity NPC284807
0.6018 Remote Similarity NPC80843
0.6 Remote Similarity NPC180550
0.6 Remote Similarity NPC35405
0.5966 Remote Similarity NPC488209
0.595 Remote Similarity NPC288205
0.595 Remote Similarity NPC51465
0.5938 Remote Similarity NPC161717
0.5897 Remote Similarity NPC481082
0.5897 Remote Similarity NPC164419
0.5862 Remote Similarity NPC473383
0.5841 Remote Similarity NPC114441
0.5833 Remote Similarity NPC187618
0.5798 Remote Similarity NPC114692
0.5785 Remote Similarity NPC475486
0.5772 Remote Similarity NPC313110
0.5763 Remote Similarity NPC131469
0.5755 Remote Similarity NPC57362
0.5726 Remote Similarity NPC151543
0.5714 Remote Similarity NPC95437
0.5702 Remote Similarity NPC120116
0.5676 Remote Similarity NPC475611
0.5667 Remote Similarity NPC236657
0.5645 Remote Similarity NPC473824
0.561 Remote Similarity NPC480939
0.561 Remote Similarity NPC280941
0.561 Remote Similarity NPC235772
0.5607 Remote Similarity NPC283849
0.5556 Remote Similarity NPC471384
0.5546 Remote Similarity NPC162574
0.5505 Remote Similarity NPC31839
0.5455 Remote Similarity NPC100383
0.5446 Remote Similarity NPC191410
0.5424 Remote Similarity NPC240734
0.5417 Remote Similarity NPC118440
0.5378 Remote Similarity NPC309714
0.5372 Remote Similarity NPC73829
0.5372 Remote Similarity NPC475504
0.5366 Remote Similarity NPC218954
0.5364 Remote Similarity NPC286347
0.5357 Remote Similarity NPC475633
0.5328 Remote Similarity NPC486563
0.5328 Remote Similarity NPC488515
0.5317 Remote Similarity NPC475119
0.5294 Remote Similarity NPC112352
0.5263 Remote Similarity NPC475472
0.5246 Remote Similarity NPC123796
0.5242 Remote Similarity NPC291903
0.5227 Remote Similarity NPC484061
0.5227 Remote Similarity NPC484062
0.5224 Remote Similarity NPC293330
0.5221 Remote Similarity NPC294112
0.5217 Remote Similarity NPC127853
0.5185 Remote Similarity NPC111466
0.5182 Remote Similarity NPC488212
0.5152 Remote Similarity NPC488211
0.5126 Remote Similarity NPC6377
0.5126 Remote Similarity NPC208381
0.512 Remote Similarity NPC486564
0.5115 Remote Similarity NPC100639
0.5115 Remote Similarity NPC471550
0.5115 Remote Similarity NPC475140
0.5111 Remote Similarity NPC65105
0.5111 Remote Similarity NPC484059
0.5111 Remote Similarity NPC484060
0.5085 Remote Similarity NPC108748
0.5082 Remote Similarity NPC251768
0.5081 Remote Similarity NPC302887
0.5081 Remote Similarity NPC484832
0.5072 Remote Similarity NPC484063
0.5072 Remote Similarity NPC484064
0.5042 Remote Similarity NPC480424
0.5041 Remote Similarity NPC192791
0.504 Remote Similarity NPC37134
0.504 Remote Similarity NPC78034
0.5039 Remote Similarity NPC76972
0.5039 Remote Similarity NPC469782
0.5039 Remote Similarity NPC204414
0.5037 Remote Similarity NPC258617

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC256909 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
NPD

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