Natural Product: NPC207887

Natural Product IDNPC207887
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ZEMPQRCIDIKAOC-VDFXADRXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968783
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 ZEMPQRCIDIKAOC-VDFXADRXSA-N
Standard InCHI InChI=1S/C58H94O26/c1-24-34(64)44(81-47-41(71)35(65)27(62)21-75-47)43(73)49(77-24)82-45-36(66)28(63)22-76-50(45)80-33-11-12-54(4)31(55(33,5)23-61)10-13-57(7)32(54)9-8-25-26-18-53(2,3)14-16-58(26,17-15-56(25,57)6)52(74)84-51-46(40(70)38(68)30(20-60)79-51)83-48-42(72)39(69)37(67)29(19-59)78-48/h8,24,26-51,59-73H,9-23H2,1-7H3/t24-,26?,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-,54?,55?,56?,57?,58?/m0/s1
SMILES C[C@H]1[C@H]([C@H]([C@H]([C@@H](O1)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[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)C1(C)CO)O)O)O)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1206.6 Volume:   1149.432
?
Van der Waals volume.
Dense:   1.05 LogP:   0.662
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.329
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.422
?
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:   0.05 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.221 Fsp3:   0.948
MCE-18:   215.327
?
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:   0.851 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:   0.101
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.264 Promiscuous compounds:   0.014

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.042 MDCK Permeability:   -4.83
Pgp-inhibitor:   0.0 Pgp-substrate:   0.454
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):   0.996
20% Bioavailability (F20%):   0.037 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.078 MRP1:   0.929
Plasma Protein Binding (PPB):   60.839% Volume Distribution (VD):   -0.323
Fu: 21.113%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.999
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:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.081
HLM stability:   0.386
?
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):  -0.839 Half-life (T1/2):  4.22

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.774 Drug-induced Liver Injury (DILI):  0.9
AMES Toxicity:  0.991 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.006 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.782 Drug-induced Nephrotoxicity:  0.975
Genotoxicity:  0.005 RPMI-8226 Immunitoxicity:  0.426
A549 Cytotoxicity:  0.998 Hek293 Cytotoxicity:  0.76
BCF:   1.527
?
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:   4.152
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.665
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.604
?
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
NPO957 Sapindus mukorossi Species Sapindaceae Eukaryota Galls n.a. n.a. PMID[16724837]
NPO957 Sapindus mukorossi Species Sapindaceae Eukaryota n.a. gall n.a. PMID[17827775]
NPO957 Sapindus mukorossi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO957 Sapindus mukorossi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO957 Sapindus mukorossi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO957 Sapindus mukorossi Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO957 Sapindus mukorossi Species Sapindaceae 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 NPC207887 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
0.8713 High Similarity NPC475504
0.8476 Intermediate Similarity NPC481078
0.8018 Intermediate Similarity NPC123199
0.7838 Intermediate Similarity NPC79643
0.7778 Intermediate Similarity NPC202828
0.7778 Intermediate Similarity NPC119592
0.7712 Intermediate Similarity NPC298034
0.7712 Intermediate Similarity NPC71065
0.7692 Intermediate Similarity NPC293330
0.7434 Intermediate Similarity NPC475287
0.7358 Intermediate Similarity NPC469946
0.7311 Intermediate Similarity NPC41061
0.7311 Intermediate Similarity NPC227551
0.729 Intermediate Similarity NPC112352
0.719 Intermediate Similarity NPC236638
0.719 Intermediate Similarity NPC294453
0.719 Intermediate Similarity NPC305981
0.7179 Intermediate Similarity NPC471550
0.7143 Intermediate Similarity NPC481079
0.7131 Intermediate Similarity NPC261506
0.7131 Intermediate Similarity NPC4328
0.7107 Intermediate Similarity NPC65105
0.7049 Intermediate Similarity NPC481081
0.696 Remote Similarity NPC250247
0.6944 Remote Similarity NPC295371
0.6937 Remote Similarity NPC63159
0.6935 Remote Similarity NPC70809
0.6891 Remote Similarity NPC191827
0.686 Remote Similarity NPC57484
0.6838 Remote Similarity NPC76972
0.6838 Remote Similarity NPC469782
0.6838 Remote Similarity NPC204414
0.6777 Remote Similarity NPC481080
0.6754 Remote Similarity NPC276093
0.6726 Remote Similarity NPC297263
0.6696 Remote Similarity NPC480475
0.656 Remote Similarity NPC43550
0.6545 Remote Similarity NPC150400
0.6529 Remote Similarity NPC135904
0.6446 Remote Similarity NPC323341
0.6441 Remote Similarity NPC31838
0.641 Remote Similarity NPC301449
0.641 Remote Similarity NPC601290
0.6357 Remote Similarity NPC224381
0.6356 Remote Similarity NPC241909
0.6316 Remote Similarity NPC309714
0.6311 Remote Similarity NPC475899
0.6311 Remote Similarity NPC133818
0.6306 Remote Similarity NPC475516
0.6281 Remote Similarity NPC60557
0.6281 Remote Similarity NPC67857
0.6271 Remote Similarity NPC324875
0.6271 Remote Similarity NPC292677
0.627 Remote Similarity NPC473452
0.627 Remote Similarity NPC110633
0.6241 Remote Similarity NPC477464
0.6231 Remote Similarity NPC220160
0.6228 Remote Similarity NPC223301
0.6228 Remote Similarity NPC171544
0.621 Remote Similarity NPC100639
0.6167 Remote Similarity NPC187290
0.6148 Remote Similarity NPC313110
0.614 Remote Similarity NPC213674
0.6133 Remote Similarity NPC469777
0.6121 Remote Similarity NPC164389
0.6121 Remote Similarity NPC46665
0.6118 Remote Similarity NPC469772
0.6116 Remote Similarity NPC75287
0.6098 Remote Similarity NPC123522
0.6091 Remote Similarity NPC90856
0.6083 Remote Similarity NPC187618
0.6083 Remote Similarity NPC480474
0.605 Remote Similarity NPC104372
0.6047 Remote Similarity NPC471385
0.6034 Remote Similarity NPC160415
0.6027 Remote Similarity NPC469775
0.6017 Remote Similarity NPC481082
0.6017 Remote Similarity NPC222580
0.6017 Remote Similarity NPC164419
0.6014 Remote Similarity NPC469774
0.6 Remote Similarity NPC166422
0.6 Remote Similarity NPC263756
0.6 Remote Similarity NPC136768
0.6 Remote Similarity NPC33012
0.6 Remote Similarity NPC219180
0.6 Remote Similarity NPC100925
0.6 Remote Similarity NPC155410
0.5984 Remote Similarity NPC85154
0.5983 Remote Similarity NPC251768
0.5983 Remote Similarity NPC473459
0.5982 Remote Similarity NPC48499
0.5973 Remote Similarity NPC469778
0.5969 Remote Similarity NPC470876
0.5963 Remote Similarity NPC256798
0.595 Remote Similarity NPC480473
0.5946 Remote Similarity NPC189884
0.5946 Remote Similarity NPC138334
0.5935 Remote Similarity NPC469773
0.5926 Remote Similarity NPC8524
0.5926 Remote Similarity NPC480422
0.5906 Remote Similarity NPC488560
0.5902 Remote Similarity NPC104137
0.5902 Remote Similarity NPC475486
0.5902 Remote Similarity NPC26626
0.5887 Remote Similarity NPC300419
0.5877 Remote Similarity NPC139894
0.5877 Remote Similarity NPC59804
0.5873 Remote Similarity NPC251263
0.5859 Remote Similarity NPC4749
0.5833 Remote Similarity NPC486563
0.5827 Remote Similarity NPC475160
0.5827 Remote Similarity NPC473714
0.5826 Remote Similarity NPC473373
0.582 Remote Similarity NPC295823
0.582 Remote Similarity NPC174720
0.582 Remote Similarity NPC475467
0.5814 Remote Similarity NPC476068
0.5812 Remote Similarity NPC192791
0.5794 Remote Similarity NPC471384
0.5785 Remote Similarity NPC114484
0.5776 Remote Similarity NPC473884
0.5772 Remote Similarity NPC36831
0.5769 Remote Similarity NPC286457
0.576 Remote Similarity NPC610204
0.5755 Remote Similarity NPC475368
0.5738 Remote Similarity NPC486564
0.5726 Remote Similarity NPC815
0.5714 Remote Similarity NPC10607
0.5714 Remote Similarity NPC159309
0.5714 Remote Similarity NPC192600
0.5714 Remote Similarity NPC302543
0.5714 Remote Similarity NPC86222
0.5705 Remote Similarity NPC295941
0.5703 Remote Similarity NPC283417
0.5703 Remote Similarity NPC200049
0.5692 Remote Similarity NPC21691
0.5691 Remote Similarity NPC69811
0.5667 Remote Similarity NPC475591
0.5667 Remote Similarity NPC236870
0.5667 Remote Similarity NPC162574
0.5664 Remote Similarity NPC214484
0.5664 Remote Similarity NPC472268
0.5649 Remote Similarity NPC480418
0.5648 Remote Similarity NPC237503
0.5635 Remote Similarity NPC268184
0.562 Remote Similarity NPC609763
0.5614 Remote Similarity NPC29069
0.561 Remote Similarity NPC218954
0.5607 Remote Similarity NPC167383
0.5603 Remote Similarity NPC174679
0.5603 Remote Similarity NPC279554
0.56 Remote Similarity NPC469776
0.5594 Remote Similarity NPC297950
0.5592 Remote Similarity NPC32723
0.5584 Remote Similarity NPC135334
0.5581 Remote Similarity NPC470218
0.5565 Remote Similarity NPC80986
0.5556 Remote Similarity NPC481323
0.5548 Remote Similarity NPC481324
0.5547 Remote Similarity NPC68767
0.553 Remote Similarity NPC473645
0.5528 Remote Similarity NPC114692
0.552 Remote Similarity NPC609281
0.5515 Remote Similarity NPC142151
0.5508 Remote Similarity NPC39211
0.5507 Remote Similarity NPC489209
0.5507 Remote Similarity NPC51099
0.5504 Remote Similarity NPC480419
0.55 Remote Similarity NPC30735
0.55 Remote Similarity NPC30289
0.5492 Remote Similarity NPC131469
0.5489 Remote Similarity NPC258617
0.5481 Remote Similarity NPC144644
0.5481 Remote Similarity NPC170407
0.5478 Remote Similarity NPC1046
0.547 Remote Similarity NPC235405
0.5447 Remote Similarity NPC95437
0.5442 Remote Similarity NPC220838
0.544 Remote Similarity NPC120116
0.5435 Remote Similarity NPC102505
0.5435 Remote Similarity NPC293031
0.5435 Remote Similarity NPC488514
0.5426 Remote Similarity NPC165204
0.5424 Remote Similarity NPC249848
0.5424 Remote Similarity NPC127056
0.5424 Remote Similarity NPC107966
0.541 Remote Similarity NPC118440
0.5407 Remote Similarity NPC477463
0.5403 Remote Similarity NPC236657
0.5401 Remote Similarity NPC267694
0.54 Remote Similarity NPC478559
0.54 Remote Similarity NPC478560
0.5398 Remote Similarity NPC128925
0.5396 Remote Similarity NPC153673
0.5391 Remote Similarity NPC204458
0.539 Remote Similarity NPC275225
0.5385 Remote Similarity NPC12288
0.5378 Remote Similarity NPC488561
0.5374 Remote Similarity NPC45606
0.5372 Remote Similarity NPC114304

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC207887 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