Natural Product: NPC11246

Natural Product IDNPC11246
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 QQJNIQAYUUHBGC-LSDHHAIUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10249666
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans
        • [CHEMONTID:0001604] Tetrahydrofuran lignans
          • [CHEMONTID:0003424] 9,9'-epoxylignans
            • [CHEMONTID:0001613] Dibenzylbutyrolactone lignans

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 QQJNIQAYUUHBGC-LSDHHAIUSA-N
Standard InCHI InChI=1S/C21H24O7/c1-25-17-8-12(4-5-16(17)22)7-15-14(11-28-21(15)24)6-13-9-18(26-2)20(23)19(10-13)27-3/h4-5,8-10,14-15,22-23H,6-7,11H2,1-3H3/t14-,15+/m0/s1
SMILES COc1cc(ccc1O)C[C@@H]1[C@@H](Cc2cc(c(c(c2)OC)O)OC)COC1=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   388.15 Volume:   389.179
?
Van der Waals volume.
Dense:   0.997 LogP:   1.768
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.901
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.01
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   18.0
TPSA:   94.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.704 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.23 Fsp3:   0.381
MCE-18:   60.931
?
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:   0
Colloidal aggregators:   0.187 Fluc inhibitor:   0.06
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.016
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.33
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.282 Promiscuous compounds:   0.251

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.214 MDCK Permeability:   -4.791
Pgp-inhibitor:   0.554 Pgp-substrate:   0.2
PAMPA:   0.004
?
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):   0.02
20% Bioavailability (F20%):   0.829 30% Bioavailability (F30%):   0.712
50% Bioavailability (F50%):   0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.973
Plasma Protein Binding (PPB):   93.264% Volume Distribution (VD):   -0.377
Fu: 8.019%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.348
BSEP inhibitor:   0.977

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.923
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.98
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.813
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.837
?
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):  4.479 Half-life (T1/2):  2.222

ADMET: Toxicity

hERG Blockers:  0.13 hERG Blockers (10um):  0.603
Human Hepatotoxicity (H-HT):  0.936 Drug-induced Liver Injury (DILI):  0.937
AMES Toxicity:  0.72 Rat Oral Acute Toxicity:  0.287
Maximum Recommended Daily Dose:  0.586 Skin Sensitization:  0.899
Carcinogencity:  0.687 Eye Corrosion:  0.003
Eye Irritation:  0.893 Respiratory Toxicity:  0.362
Drug-induced Neurotoxicity:  0.632 Ototoxicity:  0.597
Hematotoxicity:  0.573 Drug-induced Nephrotoxicity:  0.846
Genotoxicity:  0.964 RPMI-8226 Immunitoxicity:  0.252
A549 Cytotoxicity:  0.466 Hek293 Cytotoxicity:  0.606
BCF:   1.13
?
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:   3.846
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.964
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.476
?
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
NPO12176 Streptomyces olivaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[11376004]
NPO12176 Streptomyces olivaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[1367428]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[18314958]
NPO11237 Bupleurum salicifolium Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24242108]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[32100544]
NPO11237 Bupleurum salicifolium Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[7964800]
NPO12176 Streptomyces olivaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[Article]
NPO28466 Torreya nucifera Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12176 Streptomyces olivaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7991 Lactarius vellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16343 Galium album Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2582 Plagiomnium undulatum Species Mniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11400 Aster ptarmicoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8414 Crella incrustans Species Crellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7327 Aeromonas hydrophila Species Aeromonadaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO16792 Nocardia pseudobrasiliensis Species Nocardiaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO4033 Corydalis gigantea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7991 Lactarius vellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11400 Aster ptarmicoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12874 Sedum cepaea Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4033 Corydalis gigantea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7991 Lactarius vellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6669 Dysosma delavayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4033 Corydalis gigantea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9648 Maharanga bicolor Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28466 Torreya nucifera Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10354 Urbanodendron verrucosum Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16792 Nocardia pseudobrasiliensis Species Nocardiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO16343 Galium album Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12176 Streptomyces olivaceus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6669 Dysosma delavayi Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2291 Saussurea pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7991 Lactarius vellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3017 Artemisia caucasica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10719 Centrosema haitense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11237 Bupleurum salicifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11400 Aster ptarmicoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9018 Millettia rubiginosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9496 Gomphostemma crinitum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7653 Mosla japonica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7327 Aeromonas hydrophila Species Aeromonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO6235 Exobasidium vaccinii Species Exobasidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4970 Torricellia tiliifolia Species Torricelliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20210 Lophozia floerkei Species Scapaniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17456 Echinochloa esculenta Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4033 Corydalis gigantea Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3614 Echinopepon bigelovii Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12659 Hopea brevipetiolaris Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2582 Plagiomnium undulatum Species Mniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10560 Adenia fruticosa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1164 Osteospermum hyoseroides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1460 Rubus phoenicolasius Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8414 Crella incrustans Species Crellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12422 Pinus massoniana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12874 Sedum cepaea Species Crassulaceae 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 NPC11246 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 NPC273657
0.9149 High Similarity NPC68779
0.9149 High Similarity NPC108598
0.8462 Intermediate Similarity NPC106920
0.8462 Intermediate Similarity NPC15811
0.8113 Intermediate Similarity NPC300776
0.8113 Intermediate Similarity NPC176814
0.8113 Intermediate Similarity NPC4982
0.8113 Intermediate Similarity NPC606629
0.7586 Intermediate Similarity NPC216223
0.7414 Intermediate Similarity NPC282291
0.7414 Intermediate Similarity NPC166137
0.7069 Intermediate Similarity NPC145569
0.6935 Remote Similarity NPC478703
0.6935 Remote Similarity NPC478704
0.6724 Remote Similarity NPC293757
0.6724 Remote Similarity NPC668
0.6667 Remote Similarity NPC102908
0.6667 Remote Similarity NPC487680
0.6441 Remote Similarity NPC100675
0.6441 Remote Similarity NPC601691
0.6275 Remote Similarity NPC31344
0.6275 Remote Similarity NPC317769
0.6271 Remote Similarity NPC5310
0.625 Remote Similarity NPC478705
0.6038 Remote Similarity NPC223807
0.6 Remote Similarity NPC110699
0.6 Remote Similarity NPC106055
0.5972 Remote Similarity NPC299706
0.5972 Remote Similarity NPC115466
0.5972 Remote Similarity NPC61604
0.5962 Remote Similarity NPC72796
0.5902 Remote Similarity NPC606339
0.5893 Remote Similarity NPC211386
0.5806 Remote Similarity NPC485282
0.5806 Remote Similarity NPC485283
0.5806 Remote Similarity NPC485281
0.5806 Remote Similarity NPC610284
0.5645 Remote Similarity NPC486558
0.5625 Remote Similarity NPC487679
0.5625 Remote Similarity NPC487678
0.5593 Remote Similarity NPC275950
0.5556 Remote Similarity NPC67247
0.5538 Remote Similarity NPC608199
0.5517 Remote Similarity NPC173308
0.5517 Remote Similarity NPC181079
0.55 Remote Similarity NPC253481
0.55 Remote Similarity NPC253722
0.5455 Remote Similarity NPC325295
0.5455 Remote Similarity NPC120852
0.5455 Remote Similarity NPC174512
0.5455 Remote Similarity NPC76308
0.541 Remote Similarity NPC176586
0.541 Remote Similarity NPC210354
0.5397 Remote Similarity NPC282833
0.5345 Remote Similarity NPC92693
0.5333 Remote Similarity NPC205915
0.5323 Remote Similarity NPC191158
0.5323 Remote Similarity NPC177644
0.5294 Remote Similarity NPC165133
0.5294 Remote Similarity NPC242885
0.5294 Remote Similarity NPC95614
0.5294 Remote Similarity NPC193544
0.5294 Remote Similarity NPC232316
0.5254 Remote Similarity NPC40237
0.5246 Remote Similarity NPC475875
0.5238 Remote Similarity NPC610652
0.5231 Remote Similarity NPC29599
0.5211 Remote Similarity NPC252402
0.5211 Remote Similarity NPC102934
0.5172 Remote Similarity NPC110958
0.5172 Remote Similarity NPC19890
0.5156 Remote Similarity NPC476345
0.5156 Remote Similarity NPC90431
0.5147 Remote Similarity NPC281780
0.5094 Remote Similarity NPC85488
0.5094 Remote Similarity NPC603326
0.5079 Remote Similarity NPC187998
0.5079 Remote Similarity NPC257582
0.5079 Remote Similarity NPC241522

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC11246 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