Natural Product: NPC61160

Natural Product IDNPC61160
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
RSZMIQZFBLGYLQ-QWHYFGCJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101677163
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 RSZMIQZFBLGYLQ-QWHYFGCJSA-N
Standard InCHI InChI=1S/C75H52O48/c76-23-1-14(2-24(77)42(23)86)65(102)112-12-34-59(61-63(74(111)115-34)121-71(108)19-8-30(83)46(90)53(97)38(19)36-17(69(106)119-61)6-28(81)44(88)51(36)95)118-73(110)22-10-32(85)49(93)57(101)58(22)114-33-11-21-41(56(100)50(33)94)40-16(5-27(80)48(92)55(40)99)68(105)117-60-35(13-113-67(21)104)116-75(123-66(103)15-3-25(78)43(87)26(79)4-15)64-62(60)120-70(107)18-7-29(82)45(89)52(96)37(18)39-20(72(109)122-64)9-31(84)47(91)54(39)98/h1-11,34-35,59-64,74-101,111H,12-13H2/t34-,35-,59-,60-,61+,62+,63-,64-,74-,75+/m1/s1
SMILES c1c(cc(c(c1O)O)O)C(=O)OC[C@@H]1[C@H]([C@H]2[C@H]([C@H](O)O1)OC(=O)c1cc(c(c(c1-c1c(cc(c(c1O)O)O)C(=O)O2)O)O)O)OC(=O)c1cc(c(c(c1Oc1cc2c(-c3c(cc(c(c3O)O)O)C(=O)O[C@@H]3[C@@H](COC2=O)O[C@H]([C@H]2[C@H]3OC(=O)c3cc(c(c(c3-c3c(cc(c(c3O)O)O)C(=O)O2)O)O)O)OC(=O)c2cc(c(c(c2)O)O)O)c(c1O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1720.16 Volume:   1512.983
?
Van der Waals volume.
Dense:   1.137 LogP:   -1.881
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -3.088
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.538
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   97.0
TPSA:   810.6
?
Topological Polar Surface Area.
H-Bond Acceptor:   48.0
H-Bond Donor:   27.0 Rings:   14.0
Heavy Atoms:   48.0

MedChem Properties

QED Drug-Likeness Score:   0.056 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.249 Fsp3:   0.16
MCE-18:   338.299
?
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:   0.07
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.324
?
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:   0.615 Promiscuous compounds:   0.991

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -9.298 MDCK Permeability:   -4.596
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%):   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):   78.472% Volume Distribution (VD):   -0.079
Fu: 10.35%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.993
OATP1B3 inhibitor:   0.98 BCRP inhibitor:   0.545
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:   0.902
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
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):  4.056 Half-life (T1/2):  9.623

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.998
Human Hepatotoxicity (H-HT):  0.084 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  1.0 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.964 Skin Sensitization:  1.0
Carcinogencity:  0.016 Eye Corrosion:  0.0
Eye Irritation:  0.558 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.0 Drug-induced Nephrotoxicity:  0.02
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.0
A549 Cytotoxicity:  1.0 Hek293 Cytotoxicity:  0.246
BCF:   -1.028
?
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:   3.105
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.901
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.192
?
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
NPO12926 Dendrospora tenella Species n.a. Eukaryota n.a. n.a. n.a. PMID[10217713]
NPO13919 Agathis microstachya Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12771 Eucalyptus alba Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12431 Cytospora rhizophorae Species Valsaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6238 Pseudo-nitzschia multiseries Species Bacillariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10422 Penicillium thymicola Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13415 Securigera coronilla Species Romaleidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20658 Lonicera caerulea Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11384 Tibouchina semidecandra Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12926 Dendrospora tenella Species n.a. Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13091 Helianthus ciliaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7310 Corchorus trilocularis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13091 Helianthus ciliaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4425 Delphinium honanense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12926 Dendrospora tenella Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7310 Corchorus trilocularis Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10049 Coleophoma empetri Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9097 Solanum hypomalacophyllum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6238 Pseudo-nitzschia multiseries Species Bacillariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12245 Lasiosiphon burchellii Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13919 Agathis microstachya Species Araucariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12431 Cytospora rhizophorae Species Valsaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10422 Penicillium thymicola Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20658 Lonicera caerulea Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13518 Senecio stabianus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28041 Scaevola taccada Species Goodeniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11384 Tibouchina semidecandra Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13625 Salacia beddomei Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12771 Eucalyptus alba Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13415 Securigera coronilla Species Romaleidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13091 Helianthus ciliaris Species Asteraceae 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

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 NPC61160 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
0.8864 High Similarity NPC488887
0.8864 High Similarity NPC488886
0.8571 High Similarity NPC290289
0.8478 Intermediate Similarity NPC469652
0.8478 Intermediate Similarity NPC486025
0.8478 Intermediate Similarity NPC486024
0.8235 Intermediate Similarity NPC483712
0.8235 Intermediate Similarity NPC158214
0.8235 Intermediate Similarity NPC214202
0.7416 Intermediate Similarity NPC223534
0.7283 Intermediate Similarity NPC187632
0.7283 Intermediate Similarity NPC240200
0.7283 Intermediate Similarity NPC488885
0.7273 Intermediate Similarity NPC40078
0.7128 Intermediate Similarity NPC194439
0.7128 Intermediate Similarity NPC33724
0.7 Intermediate Similarity NPC112211
0.7 Intermediate Similarity NPC254925
0.6837 Remote Similarity NPC488884
0.6699 Remote Similarity NPC220876
0.6667 Remote Similarity NPC97924
0.6538 Remote Similarity NPC93065
0.6465 Remote Similarity NPC116108
0.6415 Remote Similarity NPC31208
0.6415 Remote Similarity NPC160543
0.6373 Remote Similarity NPC469649
0.6364 Remote Similarity NPC483711
0.6265 Remote Similarity NPC47521
0.619 Remote Similarity NPC43918
0.619 Remote Similarity NPC261411
0.619 Remote Similarity NPC190204
0.6118 Remote Similarity NPC469651
0.6071 Remote Similarity NPC175793
0.6071 Remote Similarity NPC159913
0.6019 Remote Similarity NPC471091
0.5981 Remote Similarity NPC260521
0.598 Remote Similarity NPC469650
0.5946 Remote Similarity NPC174140
0.5938 Remote Similarity NPC269625
0.5663 Remote Similarity NPC31034
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
0.5077 Remote Similarity NPC3474

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC61160 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