Natural Product: NPC70779

Natural Product IDNPC70779
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZCTIBYKHCKBEAP-BXJMXZPGSA-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: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 ZCTIBYKHCKBEAP-BXJMXZPGSA-N
Standard InCHI InChI=1S/C64H104O30/c1-25-36(70)40(74)43(77)53(85-25)93-50-46(80)56(88-32(21-66)48(50)91-54-44(78)41(75)47(31(20-65)87-54)90-52-42(76)38(72)29(68)22-83-52)92-49-37(71)26(2)86-55(45(49)79)94-51-39(73)30(69)23-84-57(51)89-35-12-13-60(5)33(61(35,6)24-67)11-14-63(8)34(60)10-9-27-28-19-59(3,4)15-17-64(28,58(81)82)18-16-62(27,63)7/h9,25-26,28-57,65-80H,10-24H2,1-8H3,(H,81,82)/t25-,26-,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-,53-,54-,55-,56-,57-,60?,61?,62?,63?,64?/m0/s1
SMILES C[C@H]1[C@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@@H](O[C@H](CO)[C@@H]1O[C@H]1C([C@H]([C@@H]([C@@H](CO)O1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O)O[C@@H]1[C@H]([C@H](C)O[C@H]([C@@H]1O)O[C@@H]1[C@H]([C@H](CO[C@H]1OC1CCC2(C)C(CCC3(C)C2CC=C2C4CC(C)(C)CCC4(CCC32C)C(=O)O)C1(C)CO)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1352.66 Volume:   1279.812
?
Van der Waals volume.
Dense:   1.057 LogP:   0.073
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.791
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.091
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   63.0
TPSA:   471.74
?
Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   17.0 Rings:   11.0
Heavy Atoms:   30.0

MedChem Properties

QED Drug-Likeness Score:   0.053 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.687 Fsp3:   0.953
MCE-18:   238.0
?
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:   0.818 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:   0.107
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.346 Promiscuous compounds:   0.019

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.127 MDCK Permeability:   -4.787
Pgp-inhibitor:   0.0 Pgp-substrate:   0.986
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):   0.904
20% Bioavailability (F20%):   0.002 30% Bioavailability (F30%):   0.854
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.995
Plasma Protein Binding (PPB):   52.718% Volume Distribution (VD):   -0.337
Fu: 22.512%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.522
OATP1B3 inhibitor:   0.987 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:   0.001 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:   0.012
?
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):  -1.065 Half-life (T1/2):  5.038

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.318 Drug-induced Liver Injury (DILI):  0.31
AMES Toxicity:  0.9 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.61 Drug-induced Nephrotoxicity:  0.878
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.222
A549 Cytotoxicity:  0.849 Hek293 Cytotoxicity:  0.458
BCF:   0.707
?
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:   3.667
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.326
?
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
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]
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 NPC70779 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
0.8818 High Similarity NPC133818
0.8376 Intermediate Similarity NPC471385
0.8246 Intermediate Similarity NPC251263
0.822 Intermediate Similarity NPC161717
0.8091 Intermediate Similarity NPC276093
0.7748 Intermediate Similarity NPC481082
0.7748 Intermediate Similarity NPC164419
0.7692 Intermediate Similarity NPC323341
0.7664 Intermediate Similarity NPC174679
0.7664 Intermediate Similarity NPC279554
0.7544 Intermediate Similarity NPC324875
0.7544 Intermediate Similarity NPC292677
0.7355 Intermediate Similarity NPC54636
0.7333 Intermediate Similarity NPC219180
0.719 Intermediate Similarity NPC166422
0.7182 Intermediate Similarity NPC59804
0.7027 Intermediate Similarity NPC56713
0.6875 Remote Similarity NPC202828
0.6875 Remote Similarity NPC119592
0.6752 Remote Similarity NPC139044
0.675 Remote Similarity NPC488209
0.6667 Remote Similarity NPC127056
0.6637 Remote Similarity NPC12288
0.661 Remote Similarity NPC471383
0.6557 Remote Similarity NPC475486
0.6481 Remote Similarity NPC28198
0.6481 Remote Similarity NPC476123
0.646 Remote Similarity NPC270667
0.6439 Remote Similarity NPC298034
0.6439 Remote Similarity NPC71065
0.6387 Remote Similarity NPC104400
0.6387 Remote Similarity NPC10320
0.6364 Remote Similarity NPC236638
0.6364 Remote Similarity NPC79718
0.6364 Remote Similarity NPC294453
0.6325 Remote Similarity NPC488561
0.6281 Remote Similarity NPC257468
0.6172 Remote Similarity NPC471384
0.6167 Remote Similarity NPC114304
0.6154 Remote Similarity NPC25605
0.6142 Remote Similarity NPC475287
0.6136 Remote Similarity NPC110633
0.6129 Remote Similarity NPC323359
0.608 Remote Similarity NPC488564
0.6068 Remote Similarity NPC136877
0.6016 Remote Similarity NPC76972
0.6016 Remote Similarity NPC469782
0.6016 Remote Similarity NPC475504
0.6016 Remote Similarity NPC204414
0.6015 Remote Similarity NPC473452
0.6 Remote Similarity NPC305981
0.5956 Remote Similarity NPC261506
0.5956 Remote Similarity NPC4328
0.595 Remote Similarity NPC469945
0.5946 Remote Similarity NPC204407
0.5926 Remote Similarity NPC65105
0.5917 Remote Similarity NPC6377
0.5917 Remote Similarity NPC208381
0.5893 Remote Similarity NPC283849
0.587 Remote Similarity NPC220160
0.5859 Remote Similarity NPC280941
0.5859 Remote Similarity NPC235772
0.5852 Remote Similarity NPC41061
0.5852 Remote Similarity NPC227551
0.5833 Remote Similarity NPC114441
0.5827 Remote Similarity NPC250247
0.5809 Remote Similarity NPC293330
0.5785 Remote Similarity NPC472949
0.5763 Remote Similarity NPC164194
0.5739 Remote Similarity NPC100383
0.5738 Remote Similarity NPC80843
0.5738 Remote Similarity NPC22956
0.5726 Remote Similarity NPC180550
0.5726 Remote Similarity NPC35405
0.5703 Remote Similarity NPC187618
0.5702 Remote Similarity NPC109079
0.5659 Remote Similarity NPC481078
0.5652 Remote Similarity NPC136768
0.5641 Remote Similarity NPC284807
0.5625 Remote Similarity NPC218954
0.5581 Remote Similarity NPC241909
0.5573 Remote Similarity NPC288205
0.5573 Remote Similarity NPC51465
0.5573 Remote Similarity NPC476992
0.5556 Remote Similarity NPC91838
0.5547 Remote Similarity NPC286457
0.553 Remote Similarity NPC60557
0.553 Remote Similarity NPC313110
0.553 Remote Similarity NPC67857
0.5478 Remote Similarity NPC606107
0.5469 Remote Similarity NPC488515
0.5468 Remote Similarity NPC43550
0.5414 Remote Similarity NPC469775
0.5409 Remote Similarity NPC469774
0.5407 Remote Similarity NPC135904
0.5407 Remote Similarity NPC123199
0.5401 Remote Similarity NPC481080
0.54 Remote Similarity NPC40085
0.5391 Remote Similarity NPC73829
0.5379 Remote Similarity NPC62725
0.5362 Remote Similarity NPC57484
0.5299 Remote Similarity NPC177246
0.5294 Remote Similarity NPC155410
0.529 Remote Similarity NPC488211
0.5282 Remote Similarity NPC302543
0.5274 Remote Similarity NPC488210
0.5259 Remote Similarity NPC123522
0.5259 Remote Similarity NPC79643
0.525 Remote Similarity NPC473538
0.5231 Remote Similarity NPC119794
0.5229 Remote Similarity NPC264270
0.5217 Remote Similarity NPC488560
0.5215 Remote Similarity NPC100925
0.5194 Remote Similarity NPC257964
0.5154 Remote Similarity NPC275668
0.5152 Remote Similarity NPC469777
0.5147 Remote Similarity NPC192600
0.5145 Remote Similarity NPC100639
0.5133 Remote Similarity NPC475368
0.5122 Remote Similarity NPC127853
0.512 Remote Similarity NPC475296
0.5118 Remote Similarity NPC473734
0.5113 Remote Similarity NPC295823
0.5113 Remote Similarity NPC174720
0.5113 Remote Similarity NPC475467
0.5109 Remote Similarity NPC165204
0.5105 Remote Similarity NPC481081
0.5103 Remote Similarity NPC488212
0.507 Remote Similarity NPC258617
0.506 Remote Similarity NPC469772
0.5039 Remote Similarity NPC230948
0.5038 Remote Similarity NPC486564
0.5035 Remote Similarity NPC21691
0.5031 Remote Similarity NPC469776
0.5031 Remote Similarity NPC32723

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC70779 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