Natural Product: NPC470514

Natural Product IDNPC470514
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Sorbifoliaside C
IUPAC Name (3R,4R,4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2R,3R,4S,5S,6R)-4,5-dihydroxy-3-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxy-3,4-dihydroxy-2,2,6a,6b,9,9,12a-heptamethyl-4a-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxymethyl]-3,4,6,6a,7,8,8a,10,11,12,13,14b-dodecahydro-1H-picen-5-one
Synonyms sorbifoliaside C
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2058159
PubChem CID 66552718
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 YURMATDASSYCTB-TUANEQDRSA-N
Standard InCHI InChI=1S/C60H98O30/c1-55(2)14-23-22-8-9-30-57(5)12-11-32(89-54-47(90-53-46(78)40(72)35(67)26(18-63)86-53)42(74)37(69)28(88-54)20-82-51-44(76)39(71)34(66)25(17-62)85-51)56(3,4)29(57)10-13-58(30,6)59(22,7)15-31(64)60(23,49(80)48(55)79)21-83-52-45(77)41(73)36(68)27(87-52)19-81-50-43(75)38(70)33(65)24(16-61)84-50/h8,23-30,32-54,61-63,65-80H,9-21H2,1-7H3/t23-,24+,25+,26+,27+,28+,29-,30+,32-,33+,34+,35+,36+,37+,38-,39-,40-,41-,42-,43+,44+,45+,46+,47+,48-,49-,50+,51+,52+,53-,54-,57-,58+,59+,60-/m0/s1
SMILES CC1(CC2C3=CCC4C5(CCC(C(C5CCC4(C3(CC(=O)C2(C(C1O)O)COC6C(C(C(C(O6)COC7C(C(C(C(O7)CO)O)O)O)O)O)O)C)C)(C)C)OC8C(C(C(C(O8)COC9C(C(C(C(O9)CO)O)O)O)O)O)OC1C(C(C(C(O1)CO)O)O)O)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1298.61 Volume:   1219.185
?
Van der Waals volume.
Dense:   1.065 LogP:   -2.571
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.241
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.119
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The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   57.0
TPSA:   493.74
?
Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   19.0 Rings:   10.0
Heavy Atoms:   30.0

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:   7.488 Fsp3:   0.95
MCE-18:   222.923
?
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:   0.0 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
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.396
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.423 Promiscuous compounds:   0.001

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.555 MDCK Permeability:   -4.965
Pgp-inhibitor:   0.0 Pgp-substrate:   0.999
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%):   0.857 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):   16.811% Volume Distribution (VD):   -0.345
Fu: 37.66%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.018 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.84 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.026 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.102 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):  -0.775 Half-life (T1/2):  3.869

ADMET: Toxicity

hERG Blockers:  0.004 hERG Blockers (10um):  0.202
Human Hepatotoxicity (H-HT):  0.247 Drug-induced Liver Injury (DILI):  0.258
AMES Toxicity:  0.742 Rat Oral Acute Toxicity:  0.085
Maximum Recommended Daily Dose:  0.089 Skin Sensitization:  0.002
Carcinogencity:  0.002 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.531 Ototoxicity:  1.0
Hematotoxicity:  0.001 Drug-induced Nephrotoxicity:  0.003
Genotoxicity:  0.007 RPMI-8226 Immunitoxicity:  0.149
A549 Cytotoxicity:  0.019 Hek293 Cytotoxicity:  0.965
BCF:   0.505
?
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:   3.914
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.267
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.2
?
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
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota wood n.a. n.a. PMID[10691716]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota husks Inner Mongolia, China 2004-SEP PMID[18549275]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[22801644]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota leaves n.a. n.a. PMID[23313635]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT165 Cell line HeLa Homo sapiens IC50 > 100000.0 nM PMID[15104487]
NPT547 Cell line BGC-823 Homo sapiens IC50 > 100000.0 nM PMID[1965654]
NPT83 Cell line MCF7 Homo sapiens IC50 > 100000.0 nM DrugMatrix in vivo data: Pathology
NPT306 Cell line PC-3 Homo sapiens IC50 > 100000.0 nM PubChem BioAssay data set
NPT65 Cell line HepG2 Homo sapiens IC50 > 100000.0 nM PMID[16872131]
NPT81 Cell line A549 Homo sapiens IC50 > 100000.0 nM PMID[24904961]
NPT453 Cell line HT-1080 Homo sapiens IC50 > 100000.0 nM PMID[22119124]
NPT1171 Cell line HEp-2 Homo sapiens IC50 > 100000.0 nM PMID[16180827]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 100000.0 nM PMID[22801644]

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 NPC470514 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
0.9355 High Similarity NPC470513
0.7864 Intermediate Similarity NPC470516
0.7576 Intermediate Similarity NPC470512
0.7282 Intermediate Similarity NPC173859
0.6952 Remote Similarity NPC148603
0.6909 Remote Similarity NPC470915
0.6522 Remote Similarity NPC470911
0.6422 Remote Similarity NPC470515
0.6404 Remote Similarity NPC185466
0.6271 Remote Similarity NPC470517
0.6126 Remote Similarity NPC63159
0.6087 Remote Similarity NPC207738
0.6053 Remote Similarity NPC481079
0.6038 Remote Similarity NPC48499
0.5965 Remote Similarity NPC470914
0.5776 Remote Similarity NPC291903
0.5656 Remote Similarity NPC603137
0.5652 Remote Similarity NPC222580
0.5652 Remote Similarity NPC123796
0.5625 Remote Similarity NPC469946
0.562 Remote Similarity NPC79643
0.561 Remote Similarity NPC475140
0.5583 Remote Similarity NPC475119
0.5575 Remote Similarity NPC478066
0.5537 Remote Similarity NPC473824
0.5537 Remote Similarity NPC607904
0.5537 Remote Similarity NPC610204
0.5528 Remote Similarity NPC135904
0.5526 Remote Similarity NPC480947
0.5517 Remote Similarity NPC297263
0.5484 Remote Similarity NPC470218
0.5478 Remote Similarity NPC480475
0.547 Remote Similarity NPC471435
0.547 Remote Similarity NPC471434
0.5455 Remote Similarity NPC288205
0.5455 Remote Similarity NPC51465
0.5431 Remote Similarity NPC105800
0.5417 Remote Similarity NPC31838
0.5417 Remote Similarity NPC609281
0.5403 Remote Similarity NPC123199
0.5378 Remote Similarity NPC606145
0.5372 Remote Similarity NPC606553
0.5345 Remote Similarity NPC232237
0.5339 Remote Similarity NPC119794
0.531 Remote Similarity NPC473373
0.5304 Remote Similarity NPC112352
0.5299 Remote Similarity NPC148417
0.5299 Remote Similarity NPC162574
0.5285 Remote Similarity NPC60557
0.5285 Remote Similarity NPC67857
0.528 Remote Similarity NPC609305
0.5271 Remote Similarity NPC41061
0.5271 Remote Similarity NPC227551
0.5271 Remote Similarity NPC258617
0.5259 Remote Similarity NPC309714
0.5242 Remote Similarity NPC151543
0.5231 Remote Similarity NPC43550
0.5225 Remote Similarity NPC164194
0.5221 Remote Similarity NPC208650
0.5214 Remote Similarity NPC251768
0.5214 Remote Similarity NPC164389
0.5214 Remote Similarity NPC488526
0.5191 Remote Similarity NPC305981
0.5167 Remote Similarity NPC78034
0.5164 Remote Similarity NPC469947
0.5164 Remote Similarity NPC104137
0.5164 Remote Similarity NPC26626
0.5164 Remote Similarity NPC480948
0.5161 Remote Similarity NPC610461
0.5152 Remote Similarity NPC261506
0.5152 Remote Similarity NPC4328
0.5141 Remote Similarity NPC329893
0.513 Remote Similarity NPC295371
0.513 Remote Similarity NPC220427
0.5128 Remote Similarity NPC605226
0.5126 Remote Similarity NPC470913
0.5126 Remote Similarity NPC257468
0.5122 Remote Similarity NPC480939
0.5113 Remote Similarity NPC70809
0.5086 Remote Similarity NPC263756
0.5086 Remote Similarity NPC213674
0.5083 Remote Similarity NPC64715
0.5083 Remote Similarity NPC302887
0.5083 Remote Similarity NPC484832
0.5082 Remote Similarity NPC488564
0.5082 Remote Similarity NPC160452
0.5081 Remote Similarity NPC172365
0.5079 Remote Similarity NPC165204
0.5076 Remote Similarity NPC481081
0.5075 Remote Similarity NPC220160
0.5071 Remote Similarity NPC475177
0.5043 Remote Similarity NPC192791
0.5043 Remote Similarity NPC127056
0.5043 Remote Similarity NPC485579
0.5041 Remote Similarity NPC36831
0.504 Remote Similarity NPC252657
0.504 Remote Similarity NPC88311
0.504 Remote Similarity NPC268184
0.5039 Remote Similarity NPC219180
0.5038 Remote Similarity NPC309223
0.5038 Remote Similarity NPC470876
0.5037 Remote Similarity NPC250247

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC470514 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