Natural Product: NPC488560

Natural Product IDNPC488560
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
PXFMPKJBXCYNQD-NBWKLQASSA-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]

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 PXFMPKJBXCYNQD-NBWKLQASSA-N
Standard InCHI InChI=1S/C58H94O25/c1-24-34(62)37(65)41(69)50(77-24)82-46-29(20-59)78-47(43(71)39(46)67)76-23-30-36(64)38(66)42(70)51(79-30)83-52(73)58-17-15-53(2,3)19-26(58)25-9-10-32-55(6)13-12-33(54(4,5)31(55)11-14-57(32,8)56(25,7)16-18-58)80-49-44(72)45(28(61)22-75-49)81-48-40(68)35(63)27(60)21-74-48/h9,24,26-51,59-72H,10-23H2,1-8H3/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-,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](CO)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]2C2=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]2(C)CC1)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1190.61 Volume:   1140.642
?
Van der Waals volume.
Dense:   1.044 LogP:   1.348
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.137
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.081
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   57.0
TPSA:   392.59
?
Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   14.0 Rings:   10.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.058 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.142 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:   0.804 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
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:   0.252 Promiscuous compounds:   0.07

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.808 MDCK Permeability:   -4.992
Pgp-inhibitor:   0.0 Pgp-substrate:   0.819
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):   0.999
20% Bioavailability (F20%):   0.958 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.011 MRP1:   0.002
Plasma Protein Binding (PPB):   66.487% Volume Distribution (VD):   -0.306
Fu: 16.898%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 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:   0.14
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.001
HLM stability:   0.519
?
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):  -0.694 Half-life (T1/2):  3.846

ADMET: Toxicity

hERG Blockers:  0.002 hERG Blockers (10um):  0.003
Human Hepatotoxicity (H-HT):  0.808 Drug-induced Liver Injury (DILI):  0.987
AMES Toxicity:  0.99 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.024 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.813 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.352 RPMI-8226 Immunitoxicity:  0.451
A549 Cytotoxicity:  0.988 Hek293 Cytotoxicity:  0.529
BCF:   1.701
?
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:   3.825
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.288
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.5
?
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
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota Fruits n.a. n.a. PMID[31301930]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 > 50000.0 nM PMID[31301930]

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 NPC488560 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
0.934 High Similarity NPC475160
0.934 High Similarity NPC473714
0.9126 High Similarity NPC295823
0.9126 High Similarity NPC174720
0.9126 High Similarity NPC475467
0.8909 High Similarity NPC476068
0.8649 High Similarity NPC481080
0.8435 Intermediate Similarity NPC236638
0.8435 Intermediate Similarity NPC294453
0.8411 Intermediate Similarity NPC241909
0.8151 Intermediate Similarity NPC250247
0.8108 Intermediate Similarity NPC60557
0.8108 Intermediate Similarity NPC67857
0.7966 Intermediate Similarity NPC305981
0.7917 Intermediate Similarity NPC224381
0.7899 Intermediate Similarity NPC261506
0.7899 Intermediate Similarity NPC4328
0.7895 Intermediate Similarity NPC135904
0.7815 Intermediate Similarity NPC202828
0.7815 Intermediate Similarity NPC119592
0.7797 Intermediate Similarity NPC41061
0.7797 Intermediate Similarity NPC227551
0.7731 Intermediate Similarity NPC43550
0.7667 Intermediate Similarity NPC481081
0.7647 Intermediate Similarity NPC475514
0.7565 Intermediate Similarity NPC192600
0.7541 Intermediate Similarity NPC70809
0.7478 Intermediate Similarity NPC76972
0.7478 Intermediate Similarity NPC469782
0.7478 Intermediate Similarity NPC204414
0.7453 Intermediate Similarity NPC475516
0.7431 Intermediate Similarity NPC104071
0.7381 Intermediate Similarity NPC480422
0.7364 Intermediate Similarity NPC102439
0.7317 Intermediate Similarity NPC298034
0.7317 Intermediate Similarity NPC71065
0.7288 Intermediate Similarity NPC155410
0.7288 Intermediate Similarity NPC123199
0.7273 Intermediate Similarity NPC110633
0.7264 Intermediate Similarity NPC48499
0.7227 Intermediate Similarity NPC100639
0.7213 Intermediate Similarity NPC258617
0.7193 Intermediate Similarity NPC481079
0.7154 Intermediate Similarity NPC65105
0.7143 Intermediate Similarity NPC148417
0.7119 Intermediate Similarity NPC79643
0.7097 Intermediate Similarity NPC136768
0.7059 Intermediate Similarity NPC165204
0.704 Intermediate Similarity NPC309223
0.7 Intermediate Similarity NPC295371
0.6929 Remote Similarity NPC220160
0.6842 Remote Similarity NPC63159
0.6822 Remote Similarity NPC102505
0.6822 Remote Similarity NPC488514
0.678 Remote Similarity NPC481078
0.6765 Remote Similarity NPC472268
0.6757 Remote Similarity NPC173583
0.675 Remote Similarity NPC475287
0.672 Remote Similarity NPC13998
0.6691 Remote Similarity NPC297950
0.664 Remote Similarity NPC57484
0.6609 Remote Similarity NPC46665
0.6579 Remote Similarity NPC112352
0.6528 Remote Similarity NPC469776
0.65 Remote Similarity NPC473826
0.6491 Remote Similarity NPC469946
0.6395 Remote Similarity NPC32723
0.6387 Remote Similarity NPC114484
0.6372 Remote Similarity NPC235405
0.6357 Remote Similarity NPC293330
0.6351 Remote Similarity NPC481323
0.6351 Remote Similarity NPC469778
0.6316 Remote Similarity NPC249848
0.6316 Remote Similarity NPC107966
0.6306 Remote Similarity NPC90856
0.6301 Remote Similarity NPC472269
0.6299 Remote Similarity NPC85154
0.6293 Remote Similarity NPC223301
0.6293 Remote Similarity NPC171544
0.6277 Remote Similarity NPC475368
0.6271 Remote Similarity NPC235438
0.6267 Remote Similarity NPC135334
0.625 Remote Similarity NPC104372
0.6239 Remote Similarity NPC30735
0.623 Remote Similarity NPC187290
0.6225 Remote Similarity NPC481324
0.6218 Remote Similarity NPC297263
0.6186 Remote Similarity NPC101744
0.6174 Remote Similarity NPC58448
0.6106 Remote Similarity NPC29069
0.6103 Remote Similarity NPC8524
0.6098 Remote Similarity NPC31838
0.6081 Remote Similarity NPC469775
0.6074 Remote Similarity NPC480417
0.6066 Remote Similarity NPC301449
0.6066 Remote Similarity NPC601290
0.6065 Remote Similarity NPC295941
0.6058 Remote Similarity NPC33012
0.605 Remote Similarity NPC159309
0.605 Remote Similarity NPC473459
0.605 Remote Similarity NPC86222
0.6036 Remote Similarity NPC128925
0.6032 Remote Similarity NPC123522
0.6018 Remote Similarity NPC214484
0.6016 Remote Similarity NPC470218
0.6016 Remote Similarity NPC471550
0.5985 Remote Similarity NPC161717
0.5983 Remote Similarity NPC39211
0.596 Remote Similarity NPC469774
0.5954 Remote Similarity NPC286457
0.5938 Remote Similarity NPC475209
0.5902 Remote Similarity NPC134835
0.5897 Remote Similarity NPC473373
0.5854 Remote Similarity NPC281148
0.5844 Remote Similarity NPC100925
0.5798 Remote Similarity NPC263756
0.5798 Remote Similarity NPC76497
0.5778 Remote Similarity NPC302543
0.5769 Remote Similarity NPC469777
0.5758 Remote Similarity NPC473386
0.5739 Remote Similarity NPC204458
0.5738 Remote Similarity NPC475591
0.5738 Remote Similarity NPC236870
0.5726 Remote Similarity NPC73318
0.5714 Remote Similarity NPC480418
0.5692 Remote Similarity NPC480419
0.5691 Remote Similarity NPC222580
0.569 Remote Similarity NPC1046
0.569 Remote Similarity NPC78046
0.5674 Remote Similarity NPC480421
0.5672 Remote Similarity NPC470876
0.5667 Remote Similarity NPC161674
0.566 Remote Similarity NPC469772
0.5656 Remote Similarity NPC40775
0.5656 Remote Similarity NPC10607
0.5656 Remote Similarity NPC251768
0.5656 Remote Similarity NPC488526
0.5649 Remote Similarity NPC191827
0.5635 Remote Similarity NPC80986
0.5625 Remote Similarity NPC114287
0.5606 Remote Similarity NPC471577
0.5592 Remote Similarity NPC23020
0.5591 Remote Similarity NPC104137
0.5591 Remote Similarity NPC26626
0.559 Remote Similarity NPC469773
0.5584 Remote Similarity NPC472270
0.5584 Remote Similarity NPC112492
0.5583 Remote Similarity NPC157868
0.5565 Remote Similarity NPC475504
0.5547 Remote Similarity NPC11242
0.5541 Remote Similarity NPC45606
0.5537 Remote Similarity NPC213674
0.5528 Remote Similarity NPC164389
0.552 Remote Similarity NPC601659
0.55 Remote Similarity NPC150400
0.5492 Remote Similarity NPC192791
0.5484 Remote Similarity NPC68175
0.5481 Remote Similarity NPC473452
0.5478 Remote Similarity NPC256798
0.5447 Remote Similarity NPC160415
0.5441 Remote Similarity NPC471580
0.544 Remote Similarity NPC609763
0.5407 Remote Similarity NPC21691
0.5403 Remote Similarity NPC173859
0.5403 Remote Similarity NPC148603
0.5403 Remote Similarity NPC480475
0.5397 Remote Similarity NPC469821
0.5379 Remote Similarity NPC475899
0.5372 Remote Similarity NPC480420
0.536 Remote Similarity NPC105800
0.5333 Remote Similarity NPC4749
0.5323 Remote Similarity NPC117714
0.531 Remote Similarity NPC237503
0.529 Remote Similarity NPC471385
0.5285 Remote Similarity NPC473343
0.5268 Remote Similarity NPC167383
0.5263 Remote Similarity NPC470911
0.5259 Remote Similarity NPC54636
0.5238 Remote Similarity NPC470515
0.5224 Remote Similarity NPC251263
0.521 Remote Similarity NPC189884
0.521 Remote Similarity NPC138334
0.5197 Remote Similarity NPC220838
0.5164 Remote Similarity NPC139894
0.5163 Remote Similarity NPC475584
0.5163 Remote Similarity NPC475152
0.5161 Remote Similarity NPC485563
0.5159 Remote Similarity NPC232237
0.5135 Remote Similarity NPC489208
0.5132 Remote Similarity NPC475394
0.5123 Remote Similarity NPC488203
0.5115 Remote Similarity NPC36831
0.5111 Remote Similarity NPC166422
0.5111 Remote Similarity NPC219180
0.5081 Remote Similarity NPC473884
0.5081 Remote Similarity NPC470512
0.5081 Remote Similarity NPC488516
0.5079 Remote Similarity NPC109588
0.5079 Remote Similarity NPC309714

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488560 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