Natural Product: NPC123587

Natural Product IDNPC123587
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 FQTWUNWPYHHEKJ-VVIORFSUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10971809
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds

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 FQTWUNWPYHHEKJ-VVIORFSUSA-N
Standard InCHI InChI=1S/C22H26O8/c1-25-13-5-11(21(23)17-9-29-17)6-14(26-2)19(13)20-15(27-3)7-12(8-16(20)28-4)22(24)18-10-30-18/h5-8,17-18,21-24H,9-10H2,1-4H3/t17-,18+,21-,22+
SMILES COc1cc(cc(c1c1c(cc(cc1OC)[C@H]([C@H]1CO1)O)OC)OC)[C@@H]([C@@H]1CO1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   418.16 Volume:   409.345
?
Van der Waals volume.
Dense:   1.022 LogP:   2.19
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.486
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.871
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   18.0
TPSA:   102.44
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.598 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.875 Fsp3:   0.455
MCE-18:   78.0
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.539 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.085
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.108
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.082 Promiscuous compounds:   0.76

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.89 MDCK Permeability:   -4.775
Pgp-inhibitor:   0.618 Pgp-substrate:   0.386
PAMPA:   0.112
?
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%):   0.063 30% Bioavailability (F30%):   0.013
50% Bioavailability (F50%):   0.821

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.642
Plasma Protein Binding (PPB):   36.275% Volume Distribution (VD):   0.116
Fu: 51.17%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.996 BCRP inhibitor:   0.589
BSEP inhibitor:   0.736

ADMET: Metabolism

CYP1A2-inhibitor:   0.013 CYP1A2-substrate:   0.007
CYP2C19-inhibitor:   0.941 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.012 CYP2C9-substrate:   0.271
CYP2D6-inhibitor:   0.368 CYP2D6-substrate:   0.115
CYP3A4-inhibitor:   0.99 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.247
HLM stability:   0.025
?
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):  6.996 Half-life (T1/2):  1.575

ADMET: Toxicity

hERG Blockers:  0.04 hERG Blockers (10um):  0.3
Human Hepatotoxicity (H-HT):  0.983 Drug-induced Liver Injury (DILI):  0.995
AMES Toxicity:  0.995 Rat Oral Acute Toxicity:  0.443
Maximum Recommended Daily Dose:  0.786 Skin Sensitization:  0.996
Carcinogencity:  0.767 Eye Corrosion:  0.001
Eye Irritation:  0.984 Respiratory Toxicity:  0.133
Drug-induced Neurotoxicity:  0.964 Ototoxicity:  0.457
Hematotoxicity:  0.687 Drug-induced Nephrotoxicity:  0.954
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.312
A549 Cytotoxicity:  0.58 Hek293 Cytotoxicity:  0.573
BCF:   0.791
?
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:   3.015
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.618
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.596
?
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
NPO27831 Phakellia flabellata Species Bubaridae Eukaryota n.a. n.a. n.a. DOI[10.1021/jo00445a028]
NPO29042 Vincetoxicum atratum Species Apocynaceae Eukaryota Roots n.a. n.a. PMID[11374953]
NPO28107 Penicillium expansum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15056914]
NPO28107 Penicillium expansum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15270557]
NPO27850 Trichilia catigua Species Meliaceae Eukaryota n.a. bark n.a. PMID[18020420]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[19948405]
NPO28107 Penicillium expansum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20415462]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. seed n.a. PMID[23672042]
NPO28107 Penicillium expansum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24024763]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[36483735]
NPO28333 Syzygium levinei Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38005226]
NPO28214 Phyllosticta cirsii Species Phyllostictaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28176 Russula lepida Species Russulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28158 Polygala fruticosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29042 Vincetoxicum atratum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28494 Hydroclathrus tenuis Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28525 Urginea riparia Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28425 Senecio miser Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28543 Alcyonium coralloides Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28507 Hymenoxys grandiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28228 Kielmeyera rubriflora Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27850 Trichilia catigua Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28050 Thalictrum podocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29373 Trichoplusia ni Species Noctuidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27918 Pterocarpus macrocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28107 Penicillium expansum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27973 Simaba cuneata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28158 Polygala fruticosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28050 Thalictrum podocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28176 Russula lepida Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28050 Thalictrum podocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28507 Hymenoxys grandiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29042 Vincetoxicum atratum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28158 Polygala fruticosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29042 Vincetoxicum atratum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27938 Meliosma wightii Species Sabiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11786 Cylindropuntia leptocaulis Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28228 Kielmeyera rubriflora Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29042 Vincetoxicum atratum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28443 Larix lyallii Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28651 Othonna tagetes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28333 Syzygium levinei Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27850 Trichilia catigua Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28009 Pellina semitubulosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO27891 Lethariella sinensis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28593 Pteris pedata Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27956 Eupatoriastrum nelsonii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28050 Thalictrum podocarpum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28107 Penicillium expansum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27973 Simaba cuneata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28176 Russula lepida Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28404 Chasmanthera dependens Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28461 Crepis czerepanovii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29373 Trichoplusia ni Species Noctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28479 Campanula hypopolia Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28158 Polygala fruticosa Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28494 Hydroclathrus tenuis Species Scytosiphonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28425 Senecio miser Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28214 Phyllosticta cirsii Species Phyllostictaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27906 Philadelphus coronarius Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25330 Maackia floribunda Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28668 Agave cocui Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28611 Phragmatobia fuliginosa Species Erebidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28525 Urginea riparia Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28197 Huperzia selago Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27918 Pterocarpus macrocarpus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28316 Scandix pecten-veneris Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9245 Ventilago madraspatana Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27831 Phakellia flabellata Species Bubaridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28071 Dendrobates auratus Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28282 Turbina corymbosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28507 Hymenoxys grandiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10135 Tripteris microcarpa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28372 Corydalis pallida Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28543 Alcyonium coralloides Species Alcyoniidae 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 NPC123587 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC123587 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