Natural Product: NPC110838

Natural Product IDNPC110838
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GMPPKSLKMRADRM-IUODEOHRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101846310
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0003012] Flavan-3-ols

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 GMPPKSLKMRADRM-IUODEOHRSA-N
Standard InCHI InChI=1S/C15H14O6/c16-9-2-1-7-3-12(19)15(21-13(7)6-9)8-4-10(17)14(20)11(18)5-8/h1-2,4-6,12,15-20H,3H2/t12-,15-/m1/s1
SMILES c1cc(cc2c1C[C@H]([C@@H](c1cc(c(c(c1)O)O)O)O2)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   290.08 Volume:   279.249
?
Van der Waals volume.
Dense:   1.039 LogP:   1.301
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.679
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.607
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
TPSA:   110.38
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.51 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.325 Fsp3:   0.2
MCE-18:   60.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.663 Fluc inhibitor:   0.577
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.063
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.045
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.513 Promiscuous compounds:   0.386

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.487 MDCK Permeability:   -4.959
Pgp-inhibitor:   0.0 Pgp-substrate:   0.067
PAMPA:   0.633
?
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):   0.023
20% Bioavailability (F20%):   0.996 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.018 MRP1:   0.893
Plasma Protein Binding (PPB):   81.044% Volume Distribution (VD):   0.032
Fu: 27.734%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.949
OATP1B3 inhibitor:   0.978 BCRP inhibitor:   0.132
BSEP inhibitor:   0.002

ADMET: Metabolism

CYP1A2-inhibitor:   0.971 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.073
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.007
CYP3A4-inhibitor:   0.995 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
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):  11.779 Half-life (T1/2):  2.348

ADMET: Toxicity

hERG Blockers:  0.113 hERG Blockers (10um):  0.799
Human Hepatotoxicity (H-HT):  0.548 Drug-induced Liver Injury (DILI):  0.717
AMES Toxicity:  0.633 Rat Oral Acute Toxicity:  0.466
Maximum Recommended Daily Dose:  0.8 Skin Sensitization:  1.0
Carcinogencity:  0.247 Eye Corrosion:  0.028
Eye Irritation:  0.983 Respiratory Toxicity:  0.774
Drug-induced Neurotoxicity:  0.017 Ototoxicity:  0.844
Hematotoxicity:  0.102 Drug-induced Nephrotoxicity:  0.03
Genotoxicity:  0.992 RPMI-8226 Immunitoxicity:  0.009
A549 Cytotoxicity:  0.992 Hek293 Cytotoxicity:  0.686
BCF:   0.599
?
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:   2.912
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.052
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.557
?
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
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. bark n.a. PMID[21192716]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. PMID[22466953]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. PMID[24450804]
NPO8181 Hypoxylon tinctor Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13790 Abedus herberti Species Belostomatidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12021 Artemisia incanescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10325 Boletus pini Species Boletaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29152 Caloboletus calopus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3075 Dimorphotheca aurantiaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9017 Fagus grandifolia Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13600 Ichthyothere latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26723 Lachnophyllum gossypinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12564 Sinularia facile Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8628 Strychnos erichsonii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12716 Stocksia brahuica n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO13987 Solanum sublobatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13685 Scrophularia umbrosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25479 Sabal blackburniana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9620 Rhodococcus fascians Species Nocardiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22798 Pseudofumaria lutea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12213 Perriera orientalis Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14078 Paramecium tetraurelia Species Parameciidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5383 Othonna dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6599 Neorautanenia ficifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22798 Pseudofumaria lutea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25479 Sabal blackburniana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10325 Boletus pini Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12716 Stocksia brahuica n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13685 Scrophularia umbrosa Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14078 Paramecium tetraurelia Species Parameciidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13790 Abedus herberti Species Belostomatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13726 Agrobacterium tumefaciens Species Rhizobiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO25479 Sabal blackburniana Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9357 Mitragyna inermis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6599 Neorautanenia ficifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25181 Cyperus papyrus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14381 Swertia pseudochinensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12021 Artemisia incanescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8181 Hypoxylon tinctor Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27620.1 Pteris cretica var. nervosa Varieties Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13987 Solanum sublobatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22798 Pseudofumaria lutea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5383 Othonna dentata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13600 Ichthyothere latifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3075 Dimorphotheca aurantiaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29152 Caloboletus calopus Species Boletaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9620 Rhodococcus fascians Species Nocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6062 Acacia mearnsii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26723 Lachnophyllum gossypinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9017 Fagus grandifolia Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8628 Strychnos erichsonii Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12564 Sinularia facile Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12213 Perriera orientalis Species Simaroubaceae 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 NPC110838 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
0.814 Intermediate Similarity NPC601844
0.6458 Remote Similarity NPC268266
0.6458 Remote Similarity NPC42760
0.6458 Remote Similarity NPC220825
0.6458 Remote Similarity NPC268342
0.64 Remote Similarity NPC325028
0.64 Remote Similarity NPC256346
0.64 Remote Similarity NPC606550
0.6296 Remote Similarity NPC482704
0.5625 Remote Similarity NPC93398
0.5625 Remote Similarity NPC258979
0.5625 Remote Similarity NPC8283
0.5577 Remote Similarity NPC261619
0.5577 Remote Similarity NPC61477
0.5577 Remote Similarity NPC78770
0.5577 Remote Similarity NPC219876
0.5577 Remote Similarity NPC126029
0.5577 Remote Similarity NPC15658
0.549 Remote Similarity NPC207179
0.549 Remote Similarity NPC167571
0.549 Remote Similarity NPC278552
0.5385 Remote Similarity NPC601997
0.5385 Remote Similarity NPC609211
0.5385 Remote Similarity NPC610665
0.5303 Remote Similarity NPC600630
0.5303 Remote Similarity NPC607896
0.5303 Remote Similarity NPC611369
0.5185 Remote Similarity NPC246328
0.5185 Remote Similarity NPC27532
0.5185 Remote Similarity NPC19721
0.5094 Remote Similarity NPC36016
0.5082 Remote Similarity NPC96576

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC110838 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
0.5577 Remote Similarity NPD1612 Clinical (unspecified phase)
0.5577 Remote Similarity NPD1613 Phase 4

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