Natural Product: NPC190927

Natural Product IDNPC190927
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZCCWQTVZGNRCJQ-MSDRGPICSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 102271942
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene 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 ZCCWQTVZGNRCJQ-MSDRGPICSA-N
Standard InCHI InChI=1S/C61H98O27/c1-24-36(65)40(69)44(73)51(81-24)86-48-31(23-78-26(3)62)84-50(47(76)43(48)72)80-22-30-39(68)42(71)46(75)53(83-30)88-55(77)61-18-17-56(4,5)19-28(61)27-11-12-33-58(8)15-14-35(57(6,7)32(58)13-16-59(33,9)60(27,10)20-34(61)64)85-54-49(38(67)29(63)21-79-54)87-52-45(74)41(70)37(66)25(2)82-52/h11,24-25,28-54,63-76H,12-23H2,1-10H3/t24-,25-,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-,58-,59+,60+,61+/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H](COC(=O)C)O[C@H]([C@@H]([C@H]1O)O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)OC(=O)[C@]12CCC(C)(C)C[C@H]1C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1262.63 Volume:   1207.474
?
Van der Waals volume.
Dense:   1.046 LogP:   1.119
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.716
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.311
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   58.0
TPSA:   418.89
?
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:   0.054 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.354 Fsp3:   0.934
MCE-18:   221.017
?
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:   0.769 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
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:   0.247 Promiscuous compounds:   0.184

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.428 MDCK Permeability:   -5.051
Pgp-inhibitor:   0.0 Pgp-substrate:   0.951
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):   0.586
20% Bioavailability (F20%):   0.765 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.01
Plasma Protein Binding (PPB):   55.388% Volume Distribution (VD):   -0.346
Fu: 22.635%
?
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:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.976
HLM stability:   0.015
?
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):  -0.689 Half-life (T1/2):  3.945

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.015
Human Hepatotoxicity (H-HT):  0.443 Drug-induced Liver Injury (DILI):  0.844
AMES Toxicity:  0.913 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.003 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.287 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.024 RPMI-8226 Immunitoxicity:  0.361
A549 Cytotoxicity:  0.58 Hek293 Cytotoxicity:  0.082
BCF:   0.822
?
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:   3.621
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.547
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.559
?
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
NPO22109 Streptomyces clavuligerus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[18450406]
NPO22109 Streptomyces clavuligerus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[19941870]
NPO22554 Eunicea laciniata Species Plexauridae Eukaryota n.a. Caribbean n.a. PMID[7769391]
NPO22554 Eunicea laciniata Species Plexauridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22494 Thalictrum rugosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21909 Alkanna tinctoria Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22109 Streptomyces clavuligerus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO22494 Thalictrum rugosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22494 Thalictrum rugosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21909 Alkanna tinctoria Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22494 Thalictrum rugosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5093 Centaurea hermannii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22750 Resseliella theobaldi Species Cecidomyiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22494 Thalictrum rugosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22554 Eunicea laciniata Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20517 Seseli elatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22367 Strychnos hirsuta Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO231 Phanera vahlii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21909 Alkanna tinctoria Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27908 Bathynella natans n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO22109 Streptomyces clavuligerus Species Streptomycetaceae Bacteria 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 NPC190927 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
0.7983 Intermediate Similarity NPC220160
0.7391 Intermediate Similarity NPC60557
0.7391 Intermediate Similarity NPC67857
0.728 Intermediate Similarity NPC102505
0.728 Intermediate Similarity NPC488514
0.7273 Intermediate Similarity NPC164389
0.7273 Intermediate Similarity NPC488526
0.7203 Intermediate Similarity NPC135904
0.719 Intermediate Similarity NPC13998
0.7097 Intermediate Similarity NPC309223
0.7059 Intermediate Similarity NPC475209
0.6983 Remote Similarity NPC104137
0.6983 Remote Similarity NPC26626
0.6911 Remote Similarity NPC286457
0.688 Remote Similarity NPC236638
0.688 Remote Similarity NPC294453
0.6807 Remote Similarity NPC76972
0.6807 Remote Similarity NPC469782
0.6807 Remote Similarity NPC204414
0.6754 Remote Similarity NPC63159
0.6746 Remote Similarity NPC305981
0.6721 Remote Similarity NPC283417
0.6721 Remote Similarity NPC200049
0.672 Remote Similarity NPC475514
0.6694 Remote Similarity NPC21691
0.6693 Remote Similarity NPC261506
0.6693 Remote Similarity NPC4328
0.6612 Remote Similarity NPC123522
0.661 Remote Similarity NPC295823
0.661 Remote Similarity NPC174720
0.661 Remote Similarity NPC475467
0.6587 Remote Similarity NPC41061
0.6587 Remote Similarity NPC470876
0.6587 Remote Similarity NPC227551
0.6557 Remote Similarity NPC165204
0.6549 Remote Similarity NPC76497
0.6522 Remote Similarity NPC232237
0.6519 Remote Similarity NPC489208
0.6518 Remote Similarity NPC480420
0.6491 Remote Similarity NPC112352
0.648 Remote Similarity NPC85154
0.6475 Remote Similarity NPC79643
0.6466 Remote Similarity NPC105800
0.6452 Remote Similarity NPC480423
0.6412 Remote Similarity NPC250247
0.6378 Remote Similarity NPC473452
0.6371 Remote Similarity NPC309907
0.6371 Remote Similarity NPC123199
0.6357 Remote Similarity NPC202828
0.6357 Remote Similarity NPC119592
0.6349 Remote Similarity NPC4749
0.6308 Remote Similarity NPC302543
0.6306 Remote Similarity NPC1046
0.6279 Remote Similarity NPC43550
0.6269 Remote Similarity NPC8524
0.6222 Remote Similarity NPC33012
0.6218 Remote Similarity NPC64715
0.6212 Remote Similarity NPC224381
0.6194 Remote Similarity NPC489209
0.6183 Remote Similarity NPC298034
0.6183 Remote Similarity NPC71065
0.6142 Remote Similarity NPC488560
0.6124 Remote Similarity NPC110633
0.6111 Remote Similarity NPC155410
0.6102 Remote Similarity NPC305267
0.6077 Remote Similarity NPC258617
0.6066 Remote Similarity NPC241909
0.6058 Remote Similarity NPC480421
0.6016 Remote Similarity NPC207738
0.5985 Remote Similarity NPC481081
0.5984 Remote Similarity NPC481079
0.5968 Remote Similarity NPC815
0.5938 Remote Similarity NPC475160
0.5938 Remote Similarity NPC473714
0.5923 Remote Similarity NPC57484
0.5923 Remote Similarity NPC473386
0.5918 Remote Similarity NPC485563
0.5887 Remote Similarity NPC481078
0.5852 Remote Similarity NPC482010
0.5846 Remote Similarity NPC481080
0.584 Remote Similarity NPC210729
0.584 Remote Similarity NPC82931
0.5827 Remote Similarity NPC192600
0.5826 Remote Similarity NPC475208
0.5826 Remote Similarity NPC48499
0.5814 Remote Similarity NPC100639
0.5794 Remote Similarity NPC172365
0.5789 Remote Similarity NPC293330
0.5789 Remote Similarity NPC65105
0.5769 Remote Similarity NPC471577
0.575 Remote Similarity NPC104071
0.5748 Remote Similarity NPC475287
0.5746 Remote Similarity NPC136768
0.5724 Remote Similarity NPC472270
0.5724 Remote Similarity NPC112492
0.5714 Remote Similarity NPC475584
0.5714 Remote Similarity NPC475152
0.5702 Remote Similarity NPC102439
0.5702 Remote Similarity NPC46665
0.5695 Remote Similarity NPC469776
0.5683 Remote Similarity NPC480422
0.5682 Remote Similarity NPC476068
0.568 Remote Similarity NPC69811
0.5672 Remote Similarity NPC161717
0.5669 Remote Similarity NPC114287
0.5662 Remote Similarity NPC70809
0.5649 Remote Similarity NPC481323
0.562 Remote Similarity NPC160415
0.562 Remote Similarity NPC117714
0.561 Remote Similarity NPC488517
0.5597 Remote Similarity NPC471580
0.5591 Remote Similarity NPC11242
0.5584 Remote Similarity NPC32723
0.5583 Remote Similarity NPC469946
0.5548 Remote Similarity NPC329893
0.5548 Remote Similarity NPC469778
0.5547 Remote Similarity NPC185466
0.5528 Remote Similarity NPC148417
0.5526 Remote Similarity NPC23020
0.5496 Remote Similarity NPC480419
0.5492 Remote Similarity NPC30289
0.5484 Remote Similarity NPC123796
0.5479 Remote Similarity NPC484831
0.5478 Remote Similarity NPC135334
0.5473 Remote Similarity NPC484829
0.5462 Remote Similarity NPC56713
0.5455 Remote Similarity NPC470218
0.5448 Remote Similarity NPC237191
0.5443 Remote Similarity NPC481324
0.544 Remote Similarity NPC488515
0.5436 Remote Similarity NPC233223
0.5436 Remote Similarity NPC183816
0.5436 Remote Similarity NPC43589
0.5417 Remote Similarity NPC173583
0.5414 Remote Similarity NPC25663
0.5397 Remote Similarity NPC37134
0.5395 Remote Similarity NPC311178
0.5391 Remote Similarity NPC31838
0.5385 Remote Similarity NPC238935
0.5385 Remote Similarity NPC610204
0.5374 Remote Similarity NPC484830
0.5372 Remote Similarity NPC295371
0.5362 Remote Similarity NPC144644
0.5362 Remote Similarity NPC170407
0.536 Remote Similarity NPC297263
0.5337 Remote Similarity NPC476113
0.5328 Remote Similarity NPC263756
0.5323 Remote Similarity NPC104400
0.5323 Remote Similarity NPC173859
0.5323 Remote Similarity NPC10320
0.5323 Remote Similarity NPC148603
0.5323 Remote Similarity NPC480475
0.5309 Remote Similarity NPC295941
0.5298 Remote Similarity NPC300655
0.5298 Remote Similarity NPC196874
0.5294 Remote Similarity NPC265841
0.5294 Remote Similarity NPC480418
0.529 Remote Similarity NPC469775
0.5271 Remote Similarity NPC187290
0.527 Remote Similarity NPC297950
0.5267 Remote Similarity NPC329878
0.5263 Remote Similarity NPC219180
0.5263 Remote Similarity NPC603137
0.526 Remote Similarity NPC222951
0.5253 Remote Similarity NPC322904
0.5252 Remote Similarity NPC37860
0.5244 Remote Similarity NPC469773
0.5238 Remote Similarity NPC222580
0.5235 Remote Similarity NPC472268
0.5234 Remote Similarity NPC301449
0.5234 Remote Similarity NPC488520
0.5234 Remote Similarity NPC601290
0.5226 Remote Similarity NPC488619
0.5211 Remote Similarity NPC68767
0.5211 Remote Similarity NPC480417
0.5203 Remote Similarity NPC213674
0.5197 Remote Similarity NPC471435
0.5197 Remote Similarity NPC471434
0.5197 Remote Similarity NPC484832
0.5195 Remote Similarity NPC478559
0.5195 Remote Similarity NPC478560
0.519 Remote Similarity NPC469774
0.5166 Remote Similarity NPC475394
0.5159 Remote Similarity NPC235438
0.5145 Remote Similarity NPC271610
0.5145 Remote Similarity NPC312650
0.5143 Remote Similarity NPC482012
0.5143 Remote Similarity NPC476991
0.5125 Remote Similarity NPC324933
0.5118 Remote Similarity NPC475504
0.5116 Remote Similarity NPC218954
0.5115 Remote Similarity NPC470915
0.5111 Remote Similarity NPC475140
0.5105 Remote Similarity NPC293031
0.5098 Remote Similarity NPC13989
0.5096 Remote Similarity NPC472269
0.5094 Remote Similarity NPC100612
0.5093 Remote Similarity NPC100925
0.5083 Remote Similarity NPC29069
0.5082 Remote Similarity NPC235405

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC190927 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