Natural Product: NPC489209

Natural Product IDNPC489209
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
XLMVMPAMCMCTLY-DICYXFJSSA-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 XLMVMPAMCMCTLY-DICYXFJSSA-N
Standard InCHI InChI=1S/C65H105NO30/c1-25-49(92-55-46(81)42(77)32(21-68)89-55)51(94-54-45(80)39(74)29(71)23-85-54)48(83)57(87-25)95-52-40(75)30(72)24-86-58(52)96-59(84)65-17-16-60(3,4)18-28(65)27-10-11-35-62(7)14-13-37(61(5,6)34(62)12-15-63(35,8)64(27,9)19-36(65)73)91-53-38(66-26(2)70)43(78)50(33(22-69)90-53)93-56-47(82)44(79)41(76)31(20-67)88-56/h10,25,28-58,67-69,71-83H,11-24H2,1-9H3,(H,66,70)/t25-,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-,58-,62-,63+,64+,65+/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]1OC(=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]([C@@H](CO)O1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)N=C(C)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H](CO)O1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1379.67 Volume:   1305.469
?
Van der Waals volume.
Dense:   1.057 LogP:   -0.67
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.299
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.178
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   63.0
TPSA:   484.1
?
Topological Polar Surface Area.
H-Bond Acceptor:   31.0
H-Bond Donor:   17.0 Rings:   11.0
Heavy Atoms:   31.0

MedChem Properties

QED Drug-Likeness Score:   0.023 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.849 Fsp3:   0.938
MCE-18:   238.889
?
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:   0.833 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
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:   0.165 Promiscuous compounds:   0.071

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.069 MDCK Permeability:   -4.774
Pgp-inhibitor:   0.0 Pgp-substrate:   0.915
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):   0.971
20% Bioavailability (F20%):   0.639 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.015 MRP1:   0.002
Plasma Protein Binding (PPB):   54.358% Volume Distribution (VD):   -0.31
Fu: 26.406%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.002
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:   0.997 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.973
HLM stability:   0.009
?
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):  -0.873 Half-life (T1/2):  4.188

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.995 Drug-induced Liver Injury (DILI):  0.998
AMES Toxicity:  0.995 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:  0.869 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.757 RPMI-8226 Immunitoxicity:  0.337
A549 Cytotoxicity:  0.827 Hek293 Cytotoxicity:  0.214
BCF:   0.945
?
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:   3.66
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.54
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.243
?
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
NPO40002 Acacia ligulata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[28976773]

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
NPT170 Cell line SK-MEL-28 Homo sapiens IC50 = 15000.0 nM PMID[28976773]
NPT859 Cell line HFF Homo sapiens IC50 = 14200.0 nM PMID[28976773]

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 NPC489209 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
0.9344 High Similarity NPC489208
0.768 Intermediate Similarity NPC286457
0.7647 Intermediate Similarity NPC104137
0.7647 Intermediate Similarity NPC26626
0.7244 Intermediate Similarity NPC85154
0.7209 Intermediate Similarity NPC470876
0.7132 Intermediate Similarity NPC473452
0.6984 Remote Similarity NPC123522
0.6953 Remote Similarity NPC283417
0.6953 Remote Similarity NPC200049
0.6917 Remote Similarity NPC164389
0.6691 Remote Similarity NPC220160
0.6667 Remote Similarity NPC57484
0.6614 Remote Similarity NPC815
0.6591 Remote Similarity NPC4749
0.6513 Remote Similarity NPC113620
0.6493 Remote Similarity NPC13998
0.6486 Remote Similarity NPC475584
0.6486 Remote Similarity NPC475152
0.6449 Remote Similarity NPC482010
0.6441 Remote Similarity NPC1046
0.6429 Remote Similarity NPC100612
0.6387 Remote Similarity NPC488620
0.6338 Remote Similarity NPC33012
0.6304 Remote Similarity NPC302543
0.6296 Remote Similarity NPC21691
0.6268 Remote Similarity NPC8524
0.6266 Remote Similarity NPC265699
0.6234 Remote Similarity NPC482013
0.622 Remote Similarity NPC64715
0.6173 Remote Similarity NPC174336
0.6164 Remote Similarity NPC475177
0.6149 Remote Similarity NPC484830
0.6111 Remote Similarity NPC488526
0.6107 Remote Similarity NPC210729
0.6107 Remote Similarity NPC82931
0.6099 Remote Similarity NPC142151
0.6099 Remote Similarity NPC267694
0.6084 Remote Similarity NPC51099
0.604 Remote Similarity NPC484831
0.6039 Remote Similarity NPC485563
0.6037 Remote Similarity NPC476113
0.6024 Remote Similarity NPC187497
0.6014 Remote Similarity NPC102505
0.6014 Remote Similarity NPC488514
0.5985 Remote Similarity NPC11242
0.5948 Remote Similarity NPC300655
0.5948 Remote Similarity NPC13989
0.5948 Remote Similarity NPC196874
0.5909 Remote Similarity NPC481078
0.5906 Remote Similarity NPC117714
0.5906 Remote Similarity NPC30289
0.5896 Remote Similarity NPC475287
0.5882 Remote Similarity NPC233223
0.5882 Remote Similarity NPC183816
0.5882 Remote Similarity NPC43589
0.586 Remote Similarity NPC488619
0.585 Remote Similarity NPC480421
0.5845 Remote Similarity NPC309223
0.5845 Remote Similarity NPC144644
0.5845 Remote Similarity NPC37860
0.5845 Remote Similarity NPC170407
0.5821 Remote Similarity NPC172365
0.5817 Remote Similarity NPC484829
0.5796 Remote Similarity NPC222951
0.5793 Remote Similarity NPC68767
0.5793 Remote Similarity NPC293031
0.5789 Remote Similarity NPC207738
0.5786 Remote Similarity NPC265841
0.5776 Remote Similarity NPC322904
0.5766 Remote Similarity NPC135904
0.5759 Remote Similarity NPC23020
0.5745 Remote Similarity NPC312650
0.5745 Remote Similarity NPC41061
0.5745 Remote Similarity NPC227551
0.5732 Remote Similarity NPC311178
0.5725 Remote Similarity NPC480423
0.5703 Remote Similarity NPC112352
0.5697 Remote Similarity NPC488201
0.5696 Remote Similarity NPC488618
0.5692 Remote Similarity NPC63159
0.5676 Remote Similarity NPC485562
0.5674 Remote Similarity NPC488308
0.5664 Remote Similarity NPC236638
0.5664 Remote Similarity NPC294453
0.5664 Remote Similarity NPC305981
0.566 Remote Similarity NPC475444
0.566 Remote Similarity NPC473679
0.5652 Remote Similarity NPC123199
0.5646 Remote Similarity NPC110385
0.5646 Remote Similarity NPC153673
0.5636 Remote Similarity NPC488204
0.5634 Remote Similarity NPC271610
0.5634 Remote Similarity NPC475514
0.5625 Remote Similarity NPC261506
0.5625 Remote Similarity NPC263756
0.5625 Remote Similarity NPC4328
0.5625 Remote Similarity NPC213674
0.5625 Remote Similarity NPC469946
0.5615 Remote Similarity NPC232237
0.5586 Remote Similarity NPC70809
0.5563 Remote Similarity NPC480418
0.5556 Remote Similarity NPC187290
0.5548 Remote Similarity NPC482011
0.5547 Remote Similarity NPC60557
0.5547 Remote Similarity NPC67857
0.5533 Remote Similarity NPC275225
0.5522 Remote Similarity NPC301449
0.5522 Remote Similarity NPC601290
0.5515 Remote Similarity NPC319719
0.5513 Remote Similarity NPC475394
0.5513 Remote Similarity NPC329878
0.551 Remote Similarity NPC250247
0.5507 Remote Similarity NPC79643
0.5503 Remote Similarity NPC480422
0.5493 Remote Similarity NPC237191
0.546 Remote Similarity NPC472270
0.546 Remote Similarity NPC112492
0.5455 Remote Similarity NPC324933
0.5442 Remote Similarity NPC488309
0.5435 Remote Similarity NPC610204
0.5429 Remote Similarity NPC475209
0.5414 Remote Similarity NPC297263
0.5407 Remote Similarity NPC481079
0.538 Remote Similarity NPC220838
0.5362 Remote Similarity NPC185466
0.5357 Remote Similarity NPC284449
0.5342 Remote Similarity NPC481081
0.5338 Remote Similarity NPC105800
0.5328 Remote Similarity NPC31838
0.5319 Remote Similarity NPC603137
0.5316 Remote Similarity NPC45606
0.5315 Remote Similarity NPC481080
0.5306 Remote Similarity NPC482012
0.5303 Remote Similarity NPC30735
0.5287 Remote Similarity NPC329893
0.5282 Remote Similarity NPC602995
0.5274 Remote Similarity NPC476779
0.5267 Remote Similarity NPC80843
0.5263 Remote Similarity NPC44716
0.5263 Remote Similarity NPC305267
0.5259 Remote Similarity NPC302887
0.5255 Remote Similarity NPC160452
0.5255 Remote Similarity NPC69811
0.5247 Remote Similarity NPC478559
0.5247 Remote Similarity NPC478560
0.5241 Remote Similarity NPC476780
0.5238 Remote Similarity NPC110700
0.5238 Remote Similarity NPC202828
0.5238 Remote Similarity NPC119592
0.5231 Remote Similarity NPC480420
0.5211 Remote Similarity NPC251263
0.5208 Remote Similarity NPC71391
0.5203 Remote Similarity NPC298034
0.5203 Remote Similarity NPC71065
0.5185 Remote Similarity NPC475504
0.5176 Remote Similarity NPC488200
0.5172 Remote Similarity NPC470518
0.5172 Remote Similarity NPC473386
0.517 Remote Similarity NPC43550
0.5149 Remote Similarity NPC251768
0.5149 Remote Similarity NPC2370
0.5149 Remote Similarity NPC480475
0.5145 Remote Similarity NPC295823
0.5145 Remote Similarity NPC174720
0.5145 Remote Similarity NPC475467
0.5143 Remote Similarity NPC288205
0.5143 Remote Similarity NPC51465
0.5137 Remote Similarity NPC22709
0.5137 Remote Similarity NPC110633
0.5137 Remote Similarity NPC476774
0.5135 Remote Similarity NPC476777
0.5133 Remote Similarity NPC224381
0.5116 Remote Similarity NPC475527
0.5115 Remote Similarity NPC127056
0.5111 Remote Similarity NPC475591
0.5111 Remote Similarity NPC236870
0.5108 Remote Similarity NPC475486
0.5106 Remote Similarity NPC76972
0.5106 Remote Similarity NPC200788
0.5106 Remote Similarity NPC469782
0.5106 Remote Similarity NPC204414
0.5106 Remote Similarity NPC610461
0.5102 Remote Similarity NPC258617
0.5099 Remote Similarity NPC279915
0.5075 Remote Similarity NPC605226
0.5071 Remote Similarity NPC280941
0.5071 Remote Similarity NPC235772
0.5069 Remote Similarity NPC470218
0.5069 Remote Similarity NPC475140
0.5067 Remote Similarity NPC476775
0.5066 Remote Similarity NPC476776
0.5064 Remote Similarity NPC475368
0.5038 Remote Similarity NPC76497
0.5037 Remote Similarity NPC46665
0.5035 Remote Similarity NPC475119
0.5034 Remote Similarity NPC471577
0.5031 Remote Similarity NPC485564
0.5027 Remote Similarity NPC475649

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC489209 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