Natural Product: NPC254925

Natural Product IDNPC254925
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
YPSRDTZNKOFIAJ-QHNYOMBNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2375777
PubChem CID 16131652
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 YPSRDTZNKOFIAJ-QHNYOMBNSA-N
Standard InCHI InChI=1S/C82H56O52/c83-27-1-17(2-28(84)47(27)97)71(111)129-67-65-41(15-121-75(115)21-9-31(87)49(99)55(105)43(21)45-23(77(117)127-65)11-33(89)51(101)57(45)107)123-81-69(67)131-79(119)25-13-35(91)53(103)59(109)61(25)125-63-39(95)7-20(8-40(63)96)74(114)134-82-70(132-80(120)26-14-36(92)54(104)60(110)62(26)126-64-37(93)5-19(6-38(64)94)73(113)133-81)68(130-72(112)18-3-29(85)48(98)30(86)4-18)66-42(124-82)16-122-76(116)22-10-32(88)50(100)56(106)44(22)46-24(78(118)128-66)12-34(90)52(102)58(46)108/h1-14,41-42,65-70,81-110H,15-16H2/t41-,42-,65-,66-,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](COC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)O[C@@H]2[C@@H]1OC(=O)c1cc(c(c(c1Oc1c(cc(cc1O)C(=O)O[C@H]1[C@@H]([C@H]([C@H]3[C@@H](COC(=O)c4cc(c(c(c4-c4c(cc(c(c4O)O)O)C(=O)O3)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1Oc1c(cc(cc1O)C(=O)O2)O)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1872.17 Volume:   1650.114
?
Van der Waals volume.
Dense:   1.135 LogP:   -1.881
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -3.593
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.805
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   114.0
TPSA:   866.36
?
Topological Polar Surface Area.
H-Bond Acceptor:   52.0
H-Bond Donor:   28.0 Rings:   18.0
Heavy Atoms:   52.0

MedChem Properties

QED Drug-Likeness Score:   0.067 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   8.393 Fsp3:   0.146
MCE-18:   361.34
?
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:   0.093
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.401
?
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:   0.733 Promiscuous compounds:   0.99

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -9.461 MDCK Permeability:   -4.818
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%):   0.067 30% Bioavailability (F30%):   0.18
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   1.0
Plasma Protein Binding (PPB):   74.057% Volume Distribution (VD):   0.035
Fu: 9.586%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.734
OATP1B3 inhibitor:   0.296 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:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.022
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
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):  2.128 Half-life (T1/2):  11.015

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.997
Human Hepatotoxicity (H-HT):  0.509 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  1.0 Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.981 Skin Sensitization:  1.0
Carcinogencity:  0.13 Eye Corrosion:  0.0
Eye Irritation:  0.233 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.273
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.602
BCF:   -1.251
?
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:   2.9
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.625
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.037
?
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
NPO20417 Tamarix nilotica Species Tamaricaceae Eukaryota n.a. n.a. n.a. PMID[20405847]
NPO20417 Tamarix nilotica Species Tamaricaceae Eukaryota n.a. n.a. n.a. PMID[23675651]
NPO20417 Tamarix nilotica Species Tamaricaceae Eukaryota Leaves n.a. n.a. PMID[26938659]
NPO20417 Tamarix nilotica Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20417 Tamarix nilotica Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20417 Tamarix nilotica Species Tamaricaceae 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
NPT116 Cell line HL-60 Homo sapiens CC50 = 55900.0 nM PubChem BioAssay data set
NPT2394 Cell line HSC-4 Homo sapiens CC50 = 43000.0 nM PubChem BioAssay data set
NPT2385 Cell line HSC-3 Homo sapiens CC50 = 47800.0 nM DrugMatrix in vitro pharmacology data
NPT924 Cell line HSC-2 Homo sapiens CC50 = 23000.0 nM DrugMatrix in vitro pharmacology data

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 NPC254925 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
1.0 High Similarity NPC112211
0.8974 High Similarity NPC194439
0.8974 High Similarity NPC33724
0.8537 High Similarity NPC488884
0.8101 Intermediate Similarity NPC290289
0.7975 Intermediate Similarity NPC223534
0.7975 Intermediate Similarity NPC483712
0.7975 Intermediate Similarity NPC158214
0.7975 Intermediate Similarity NPC214202
0.7805 Intermediate Similarity NPC187632
0.7805 Intermediate Similarity NPC240200
0.7805 Intermediate Similarity NPC488885
0.7692 Intermediate Similarity NPC31208
0.7692 Intermediate Similarity NPC160543
0.7595 Intermediate Similarity NPC40078
0.7571 Intermediate Similarity NPC43918
0.7571 Intermediate Similarity NPC261411
0.7571 Intermediate Similarity NPC190204
0.7465 Intermediate Similarity NPC469651
0.7429 Intermediate Similarity NPC47521
0.7191 Intermediate Similarity NPC488887
0.7191 Intermediate Similarity NPC488886
0.6923 Remote Similarity NPC469649
0.6905 Remote Similarity NPC97924
0.6882 Remote Similarity NPC469652
0.6882 Remote Similarity NPC486025
0.6882 Remote Similarity NPC486024
0.6737 Remote Similarity NPC93065
0.6737 Remote Similarity NPC220876
0.6304 Remote Similarity NPC116108
0.6289 Remote Similarity NPC260521
0.6238 Remote Similarity NPC174140
0.617 Remote Similarity NPC471091
0.6056 Remote Similarity NPC114791
0.6056 Remote Similarity NPC104222
0.6056 Remote Similarity NPC210501
0.6056 Remote Similarity NPC318826
0.6056 Remote Similarity NPC141331
0.5714 Remote Similarity NPC8940
0.5385 Remote Similarity NPC269625
0.5366 Remote Similarity NPC302170
0.5366 Remote Similarity NPC311389
0.5301 Remote Similarity NPC149300
0.5258 Remote Similarity NPC189312
0.5192 Remote Similarity NPC201814
0.5062 Remote Similarity NPC175793
0.5062 Remote Similarity NPC159913

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC254925 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