Natural Product: NPC319719

Natural Product IDNPC319719
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Albizoside B
IUPAC Name [(2S,3R,4S,5S,6R)-3-[(2S,3R,4S,5S,6S)-5-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-6-methyl-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl] (3S,4aR,5R,6aR,6aS,6bR,8aR,10S,12aR,14bS)-3-[(2E,6S)-6-[(2S,3R,4R,5S,6R)-5-[(2E,6S)-6-[(2S,3R,4S,5S,6R)-4,5-dihydroxy-3-[(2E,6S)-2-(hydroxymethyl)-6-methyl-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyocta-2,7-dienoyl]oxy-6-methyloxan-2-yl]oxy-2,6-dimethylocta-2,7-dienoyl]oxy-3,4-dihydroxy-6-methyloxan-2-yl]oxy-2-(hydroxymethyl)-6-methylocta-2,7-dienoyl]oxy-10-[(2R,3R,4S,5S,6R)-6-[[(2R,3R,4S,5R,6R)-4,5-dihydroxy-6-methyl-3-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxymethyl]-4,5-dihydroxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-5-hydroxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms albizoside B
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL562646
PubChem CID 42639815
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

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 JOEVSZGZFHWRGR-KTPAMDGSSA-N
Standard InCHI InChI=1S/C124H196O61/c1-20-118(14,183-109-91(154)79(142)70(133)50(5)163-109)35-25-28-56(42-126)103(159)176-100-83(146)72(135)52(7)165-114(100)185-120(16,22-3)33-23-26-49(4)101(157)175-94-53(8)167-110(92(155)86(94)149)184-119(15,21-2)34-24-27-55(41-125)102(158)173-69-40-124(115(160)182-113-99(84(147)76(139)62(45-129)171-113)181-108-93(156)96(178-106-89(152)80(143)74(137)60(43-127)168-106)95(54(9)166-108)177-105-88(151)77(140)63(46-130)170-105)58(38-116(69,10)11)57-29-30-66-121(17)36-32-68(117(12,13)65(121)31-37-122(66,18)123(57,19)39-67(124)132)174-112-98(180-107-90(153)81(144)75(138)61(44-128)169-107)85(148)78(141)64(172-112)48-162-111-97(82(145)71(134)51(6)164-111)179-104-87(150)73(136)59(131)47-161-104/h20-22,26-29,50-54,58-100,104-114,125-156H,1-3,23-25,30-48H2,4-19H3/b49-26+,55-27+,56-28+/t50-,51-,52-,53-,54+,58+,59-,60-,61-,62-,63+,64-,65+,66-,67-,68+,69+,70-,71+,72-,73+,74-,75-,76-,77+,78-,79+,80+,81+,82+,83+,84+,85+,86-,87-,88-,89-,90-,91-,92-,93-,94-,95+,96+,97-,98-,99-,100-,104+,105+,106+,107+,108+,109+,110+,111-,112+,113+,114+,118-,119-,120-,121+,122-,123-,124-/m1/s1
SMILES CC1C(C(C(C(O1)OC(C)(CCC=C(CO)C(=O)OC2C(C(C(OC2OC(C)(CCC=C(C)C(=O)OC3C(OC(C(C3O)O)OC(C)(CCC=C(CO)C(=O)OC4CC5(C(CC4(C)C)C6=CCC7C8(CCC(C(C8CCC7(C6(CC5O)C)C)(C)C)OC9C(C(C(C(O9)COC1C(C(C(C(O1)C)O)O)OC1C(C(C(CO1)O)O)O)O)O)OC1C(C(C(C(O1)CO)O)O)O)C)C(=O)OC1C(C(C(C(O1)CO)O)O)OC1C(C(C(C(O1)C)OC1C(C(C(O1)CO)O)O)OC1C(C(C(C(O1)CO)O)O)O)O)C=C)C)C=C)C)O)O)C=C)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   2661.22 Volume:   2523.558
?
Van der Waals volume.
Dense:   1.055 LogP:   -1.307
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.321
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.059
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   51.0 Rigid Bonds:   101.0
TPSA:   946.39
?
Topological Polar Surface Area.
H-Bond Acceptor:   61.0
H-Bond Donor:   32.0 Rings:   16.0
Heavy Atoms:   61.0

MedChem Properties

QED Drug-Likeness Score:   0.009 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   9.323 Fsp3:   0.855
MCE-18:   375.374
?
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:   0.001 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.0
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.38
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.425 Promiscuous compounds:   0.0

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.326 MDCK Permeability:   -4.714
Pgp-inhibitor:   0.0 Pgp-substrate:   1.0
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):   1.0
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   -6.409% Volume Distribution (VD):   -0.415
Fu: 40.326%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.064 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:   1.0 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:   0.0
HLM stability:   0.0
?
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):  -3.915 Half-life (T1/2):  8.432

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.052
Human Hepatotoxicity (H-HT):  0.177 Drug-induced Liver Injury (DILI):  0.195
AMES Toxicity:  0.794 Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.008 Skin Sensitization:  0.004
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.113 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.001
Genotoxicity:  0.006 RPMI-8226 Immunitoxicity:  0.526
A549 Cytotoxicity:  0.002 Hek293 Cytotoxicity:  0.998
BCF:   -0.904
?
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:   4.544
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.753
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.461
?
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
NPO1500 Albizia chinensis Species Fabaceae Eukaryota n.a. stem n.a. PMID[19256478]
NPO1500 Albizia chinensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1500 Albizia chinensis Species Fabaceae 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
NPT180 Cell line HCT-8 Homo sapiens IC50 = 1300.0 nM PMID[19256478]
NPT181 Cell line Bel-7402 Homo sapiens IC50 = 1300.0 nM PMID[19256478]
NPT547 Cell line BGC-823 Homo sapiens IC50 = 3800.0 nM PMID[19256478]
NPT81 Cell line A549 Homo sapiens IC50 = 300.0 nM PMID[19256478]
NPT179 Cell line A2780 Homo sapiens IC50 = 1200.0 nM PMID[19256478]

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 NPC319719 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
0.9514 High Similarity NPC324933
0.9433 High Similarity NPC222951
0.931 High Similarity NPC322904
0.9149 High Similarity NPC300655
0.9149 High Similarity NPC196874
0.8958 High Similarity NPC311178
0.8873 High Similarity NPC329878
0.8742 High Similarity NPC265699
0.8681 High Similarity NPC233223
0.8681 High Similarity NPC183816
0.8681 High Similarity NPC43589
0.8611 High Similarity NPC484829
0.8601 High Similarity NPC329893
0.8571 High Similarity NPC478559
0.8571 High Similarity NPC478560
0.8481 Intermediate Similarity NPC187497
0.8477 Intermediate Similarity NPC100612
0.8333 Intermediate Similarity NPC475444
0.8333 Intermediate Similarity NPC473679
0.8228 Intermediate Similarity NPC174336
0.8224 Intermediate Similarity NPC113620
0.8176 Intermediate Similarity NPC220838
0.7812 Intermediate Similarity NPC488201
0.7748 Intermediate Similarity NPC45606
0.755 Intermediate Similarity NPC484830
0.7467 Intermediate Similarity NPC475177
0.7434 Intermediate Similarity NPC484831
0.7423 Intermediate Similarity NPC488202
0.7423 Intermediate Similarity NPC488204
0.7089 Intermediate Similarity NPC13989
0.7048 Intermediate Similarity NPC488203
0.7006 Intermediate Similarity NPC488200
0.6552 Remote Similarity NPC488513
0.6503 Remote Similarity NPC207738
0.6471 Remote Similarity NPC488620
0.6023 Remote Similarity NPC488618
0.6 Remote Similarity NPC470876
0.5988 Remote Similarity NPC488619
0.5894 Remote Similarity NPC123522
0.5833 Remote Similarity NPC286457
0.5795 Remote Similarity NPC472270
0.5795 Remote Similarity NPC112492
0.5753 Remote Similarity NPC105800
0.5687 Remote Similarity NPC309223
0.5644 Remote Similarity NPC102505
0.5644 Remote Similarity NPC488514
0.5556 Remote Similarity NPC172365
0.5537 Remote Similarity NPC23020
0.5515 Remote Similarity NPC489209
0.5506 Remote Similarity NPC482013
0.5503 Remote Similarity NPC489208
0.5449 Remote Similarity NPC33012
0.5437 Remote Similarity NPC473452
0.5425 Remote Similarity NPC104137
0.5425 Remote Similarity NPC26626
0.5389 Remote Similarity NPC8524
0.5333 Remote Similarity NPC220160
0.5316 Remote Similarity NPC603137
0.5312 Remote Similarity NPC85154
0.5267 Remote Similarity NPC232237
0.5195 Remote Similarity NPC481079
0.5192 Remote Similarity NPC470915
0.5159 Remote Similarity NPC185466
0.5127 Remote Similarity NPC473824
0.5114 Remote Similarity NPC472268
0.5096 Remote Similarity NPC210729
0.5096 Remote Similarity NPC82931
0.509 Remote Similarity NPC70809
0.5066 Remote Similarity NPC164389
0.5061 Remote Similarity NPC13998
0.506 Remote Similarity NPC224381
0.5031 Remote Similarity NPC610204

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC319719 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