Natural Product: NPC488887

Natural Product IDNPC488887
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
FJDUJQOYRAWLJI-OXHLMTFOSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 16142269
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 FJDUJQOYRAWLJI-OXHLMTFOSA-N
Standard InCHI InChI=1S/C75H54O48/c76-25-1-16(2-26(77)44(25)88)65(102)119-61-59-38(14-112-69(106)20-9-32(83)48(92)53(97)40(20)42-22(71(108)117-59)11-34(85)50(94)55(42)99)115-74(111)63(61)121-73(110)24-13-36(87)52(96)57(101)58(24)114-37-8-19(7-31(82)47(37)91)68(105)123-75-64(122-67(104)18-5-29(80)46(90)30(81)6-18)62(120-66(103)17-3-27(78)45(89)28(79)4-17)60-39(116-75)15-113-70(107)21-10-33(84)49(93)54(98)41(21)43-23(72(109)118-60)12-35(86)51(95)56(43)100/h1-13,38-39,59-64,74-101,111H,14-15H2/t38-,39-,59-,60-,61+,62+,63-,64-,74-,75+/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]([C@@H]1OC(=O)c1cc(c(c(c1Oc1cc(cc(c1O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@H]2[C@@H](COC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)O1)OC(=O)c1cc(c(c(c1)O)O)O)OC(=O)c1cc(c(c(c1)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1722.18 Volume:   1521.54
?
Van der Waals volume.
Dense:   1.132 LogP:   -1.326
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -2.457
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.353
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   91.0
TPSA:   810.6
?
Topological Polar Surface Area.
H-Bond Acceptor:   48.0
H-Bond Donor:   27.0 Rings:   13.0
Heavy Atoms:   48.0

MedChem Properties

QED Drug-Likeness Score:   0.047 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.995 Fsp3:   0.16
MCE-18:   324.31
?
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:   0.068
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.378
?
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:   0.613 Promiscuous compounds:   0.991

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -9.498 MDCK Permeability:   -4.492
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%):   0.999 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):   75.895% Volume Distribution (VD):   -0.075
Fu: 9.284%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.997
OATP1B3 inhibitor:   0.96 BCRP inhibitor:   0.109
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.042
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.012
?
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):  4.246 Half-life (T1/2):  9.055

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.999
Human Hepatotoxicity (H-HT):  0.106 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.999 Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.992 Skin Sensitization:  1.0
Carcinogencity:  0.016 Eye Corrosion:  0.0
Eye Irritation:  0.826 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.0
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.347
BCF:   -1.048
?
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:   3.131
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.817
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.183
?
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]
NPO20786 Tamarix tetrandra Species Tamaricaceae Eukaryota Leaves n.a. n.a. PMID[26938659]
NPO20417 Tamarix nilotica Species Tamaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20786 Tamarix tetrandra 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]
NPO20786 Tamarix tetrandra 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 = 19500.0 nM PMID[26938659]
NPT2394 Cell line HSC-4 Homo sapiens CC50 = 37900.0 nM PMID[26938659]
NPT2385 Cell line HSC-3 Homo sapiens CC50 = 32600.0 nM PMID[26938659]
NPT924 Cell line HSC-2 Homo sapiens CC50 = 17700.0 nM PMID[26938659]
NPT2 Others Unspecified n.a. CC50 > 100000.0 nM PMID[26938659]
NPT2 Others Unspecified n.a. CC50 = 86600.0 nM PMID[26938659]
NPT2 Others Unspecified n.a. CC50 = 92000.0 nM PMID[26938659]

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 NPC488887 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 NPC488886
0.954 High Similarity NPC469652
0.954 High Similarity NPC486025
0.954 High Similarity NPC486024
0.8452 Intermediate Similarity NPC223534
0.8276 Intermediate Similarity NPC187632
0.8276 Intermediate Similarity NPC240200
0.8276 Intermediate Similarity NPC488885
0.8095 Intermediate Similarity NPC40078
0.809 Intermediate Similarity NPC194439
0.809 Intermediate Similarity NPC33724
0.7742 Intermediate Similarity NPC488884
0.7727 Intermediate Similarity NPC290289
0.7614 Intermediate Similarity NPC483712
0.7614 Intermediate Similarity NPC158214
0.7614 Intermediate Similarity NPC214202
0.7416 Intermediate Similarity NPC97924
0.7374 Intermediate Similarity NPC93065
0.7374 Intermediate Similarity NPC220876
0.7228 Intermediate Similarity NPC31208
0.7228 Intermediate Similarity NPC160543
0.7191 Intermediate Similarity NPC112211
0.7191 Intermediate Similarity NPC254925
0.6765 Remote Similarity NPC260521
0.6698 Remote Similarity NPC174140
0.6667 Remote Similarity NPC471091
0.6535 Remote Similarity NPC469649
0.6386 Remote Similarity NPC43918
0.6386 Remote Similarity NPC261411
0.6386 Remote Similarity NPC190204
0.631 Remote Similarity NPC469651
0.6265 Remote Similarity NPC47521
0.6265 Remote Similarity NPC175793
0.6265 Remote Similarity NPC159913
0.6139 Remote Similarity NPC469650
0.598 Remote Similarity NPC116108
0.5882 Remote Similarity NPC483711
0.5663 Remote Similarity NPC31034
0.5455 Remote Similarity NPC269625
0.5221 Remote Similarity NPC486110
0.5119 Remote Similarity NPC114791
0.5119 Remote Similarity NPC104222
0.5119 Remote Similarity NPC210501
0.5119 Remote Similarity NPC318826
0.5119 Remote Similarity NPC141331
0.5054 Remote Similarity NPC149300
0.5041 Remote Similarity NPC76264

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC488887 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