Natural Product: NPC97924

Natural Product IDNPC97924
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
FFZOOOCGCNFHAQ-GWOIDVGPSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL508647
PubChem CID 16130897
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

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 FFZOOOCGCNFHAQ-GWOIDVGPSA-N
Standard InCHI InChI=1S/C82H54O52/c83-23-1-14(2-24(84)45(23)93)71(112)133-81-70-68(130-77(118)20-9-30(90)50(98)57(105)39(20)41-22(79(120)132-70)11-32(92)52(100)59(41)107)65-35(126-81)13-123-74(115)17-6-27(87)53(101)60(108)42(17)43-44(80(121)128-65)66(63(111)62(110)61(43)109)124-33-4-15(3-25(85)46(33)94)72(113)134-82-69-67(129-76(117)19-8-29(89)49(97)56(104)38(19)40-21(78(119)131-69)10-31(91)51(99)58(40)106)64-34(125-82)12-122-73(114)16-5-26(86)47(95)54(102)36(16)37-18(75(116)127-64)7-28(88)48(96)55(37)103/h1-11,34-35,64-65,67-70,81-111H,12-13H2/t34-,35-,64-,65-,67+,68+,69-,70-,81-,82+/m1/s1
SMILES c1c(cc(c(c1O)O)O)C(=O)O[C@@H]1[C@H]2[C@H]([C@H]3[C@@H](COC(=O)c4cc(c(c(c4-c4c(c(c(c(c4O)O)O)Oc4cc(cc(c4O)O)C(=O)O[C@H]4[C@H]5[C@H]([C@H]6[C@@H](COC(=O)c7cc(c(c(c7-c7c(cc(c(c7O)O)O)C(=O)O6)O)O)O)O4)OC(=O)c4cc(c(c(c4-c4c(cc(c(c4O)O)O)C(=O)O5)O)O)O)C(=O)O3)O)O)O)O1)OC(=O)c1cc(c(c(c1-c1c(cc(c(c1O)O)O)C(=O)O2)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1870.16 Volume:   1641.557
?
Van der Waals volume.
Dense:   1.139 LogP:   -1.757
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -3.621
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.884
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   112.0
TPSA:   877.36
?
Topological Polar Surface Area.
H-Bond Acceptor:   52.0
H-Bond Donor:   29.0 Rings:   16.0
Heavy Atoms:   52.0

MedChem Properties

QED Drug-Likeness Score:   0.064 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.221 Fsp3:   0.146
MCE-18:   380.872
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   1.0 Fluc inhibitor:   0.03
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.058
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.667
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.746 Promiscuous compounds:   0.979

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -9.441 MDCK Permeability:   -4.966
Pgp-inhibitor:   0.0 Pgp-substrate:   0.0
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):   0.0
20% Bioavailability (F20%):   0.912 30% Bioavailability (F30%):   0.996
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   79.955% Volume Distribution (VD):   -0.062
Fu: 9.158%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.876
OATP1B3 inhibitor:   0.691 BCRP inhibitor:   0.021
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:   0.032
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
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):  2.569 Half-life (T1/2):  11.652

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.998
Human Hepatotoxicity (H-HT):  0.444 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  1.0 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.959 Skin Sensitization:  1.0
Carcinogencity:  0.052 Eye Corrosion:  0.0
Eye Irritation:  0.263 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.489
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.275
BCF:   -1.437
?
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:   2.921
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.814
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.126
?
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
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. PMID[ 10835233]
NPO19774 Rubus idaeus Species n.a. n.a. Fruit n.a. n.a. DOI[10.1016/S0963-9969(99)00095-2]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. PMID[21381697]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. PMID[37570937]
NPO19700 Aconitum talassicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO26422 Rubus chingii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18930 Rubus coreanus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19774 Rubus idaeus Species n.a. n.a. Fruits n.a. Database[FooDB]
NPO19774 Rubus idaeus Species n.a. n.a. Fruit n.a. n.a. Database[FooDB]
NPO19774 Rubus idaeus Species n.a. n.a. Leaf n.a. n.a. Database[FooDB]
NPO19774 Rubus idaeus Species n.a. n.a. Seed n.a. n.a. Database[FooDB]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. Database[FooDB]
NPO19700 Aconitum talassicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. Database[Phenol-Explorer]
NPO19774 Rubus idaeus Species n.a. n.a. Fruits n.a. Database[Phenol-Explorer]
NPO19700 Aconitum talassicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO19700 Aconitum talassicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26422 Rubus chingii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18930 Rubus coreanus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26422 Rubus chingii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24812 Jaspis coriacea Species Ancorinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25161 Peteravenia malvaefolia n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO24873 Anaphalis subumbellata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10415 Paraphaeosphaeria minitans Species Didymosphaeriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19774 Rubus idaeus Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19700 Aconitum talassicum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26422 Rubus chingii Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18930 Rubus coreanus Species Rosaceae 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
NPO19774 Rubus idaeus n.a. Fruits 76.1 n.a. n.a. mg/100g of FW Database [Phenol-Explorer]

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
NPT737 Cell line HUVEC Homo sapiens Inhibition = 41.5 % PMID[27237777]
NPT737 Cell line HUVEC Homo sapiens Activity = 37.6 % PMID[27237777]
NPT82 Cell line MDA-MB-231 Homo sapiens Activity = 40.7 % PMID[28835347]
NPT83 Cell line MCF7 Homo sapiens Activity = 33.7 % PMID[28835347]
NPT82 Cell line MDA-MB-231 Homo sapiens Activity = 63.0 % PMID[28835347]
NPT83 Cell line MCF7 Homo sapiens Activity = 69.0 % PMID[28835347]

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 NPC97924 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
0.878 High Similarity NPC471091
0.8462 Intermediate Similarity NPC223534
0.8312 Intermediate Similarity NPC40078
0.8272 Intermediate Similarity NPC187632
0.8272 Intermediate Similarity NPC240200
0.8049 Intermediate Similarity NPC488885
0.7857 Intermediate Similarity NPC194439
0.7857 Intermediate Similarity NPC33724
0.7561 Intermediate Similarity NPC483712
0.7561 Intermediate Similarity NPC158214
0.7561 Intermediate Similarity NPC214202
0.75 Intermediate Similarity NPC488884
0.747 Intermediate Similarity NPC290289
0.7416 Intermediate Similarity NPC488887
0.7416 Intermediate Similarity NPC488886
0.7283 Intermediate Similarity NPC469652
0.7283 Intermediate Similarity NPC486025
0.7283 Intermediate Similarity NPC486024
0.7222 Intermediate Similarity NPC47521
0.7128 Intermediate Similarity NPC93065
0.7128 Intermediate Similarity NPC220876
0.7123 Intermediate Similarity NPC43918
0.7123 Intermediate Similarity NPC261411
0.7123 Intermediate Similarity NPC190204
0.7027 Intermediate Similarity NPC469651
0.7021 Intermediate Similarity NPC260521
0.6905 Remote Similarity NPC112211
0.6905 Remote Similarity NPC254925
0.6804 Remote Similarity NPC31208
0.6804 Remote Similarity NPC160543
0.66 Remote Similarity NPC174140
0.6421 Remote Similarity NPC469649
0.6344 Remote Similarity NPC116108
0.5957 Remote Similarity NPC189312
0.5676 Remote Similarity NPC114791
0.5676 Remote Similarity NPC104222
0.5676 Remote Similarity NPC210501
0.5676 Remote Similarity NPC318826
0.5676 Remote Similarity NPC141331
0.5542 Remote Similarity NPC149300
0.5402 Remote Similarity NPC8940
0.5094 Remote Similarity NPC201814
0.5059 Remote Similarity NPC302170
0.5059 Remote Similarity NPC311389

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC97924 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