Natural Product: NPC292276

Natural Product IDNPC292276
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NHMQFXVUBRIQLN-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001615] Flavones

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 NHMQFXVUBRIQLN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H12O7/c1-8(18)23-15-4-9(2-3-11(15)20)14-7-13(22)17-12(21)5-10(19)6-16(17)24-14/h2-7,19-21H,1H3
SMILES CC(=O)Oc1cc(ccc1O)c1cc(=O)c2c(cc(cc2o1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   328.06 Volume:   314.722
?
Van der Waals volume.
Dense:   1.042 LogP:   2.436
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.221
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.054
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   19.0
TPSA:   117.2
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.488 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.485 Fsp3:   0.059
MCE-18:   19.0
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.558 Fluc inhibitor:   0.754
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.975
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.726
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.473 Promiscuous compounds:   0.667

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.217 MDCK Permeability:   -4.798
Pgp-inhibitor:   0.284 Pgp-substrate:   0.679
PAMPA:   0.3
?
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):   0.007
20% Bioavailability (F20%):   0.901 30% Bioavailability (F30%):   0.994
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.003 MRP1:   0.859
Plasma Protein Binding (PPB):   97.27% Volume Distribution (VD):   -0.584
Fu: 3.18%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.92
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.937
BSEP inhibitor:   0.905

ADMET: Metabolism

CYP1A2-inhibitor:   0.597 CYP1A2-substrate:   0.373
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.004
CYP2C9-inhibitor:   0.476 CYP2C9-substrate:   0.965
CYP2D6-inhibitor:   0.988 CYP2D6-substrate:   0.932
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.004
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.996
HLM stability:   0.765
?
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):  4.486 Half-life (T1/2):  0.99

ADMET: Toxicity

hERG Blockers:  0.026 hERG Blockers (10um):  0.369
Human Hepatotoxicity (H-HT):  0.347 Drug-induced Liver Injury (DILI):  0.839
AMES Toxicity:  0.638 Rat Oral Acute Toxicity:  0.603
Maximum Recommended Daily Dose:  0.812 Skin Sensitization:  0.853
Carcinogencity:  0.577 Eye Corrosion:  0.586
Eye Irritation:  0.997 Respiratory Toxicity:  0.722
Drug-induced Neurotoxicity:  0.029 Ototoxicity:  0.053
Hematotoxicity:  0.073 Drug-induced Nephrotoxicity:  0.012
Genotoxicity:  0.983 RPMI-8226 Immunitoxicity:  0.046
A549 Cytotoxicity:  0.605 Hek293 Cytotoxicity:  0.7
BCF:   1.01
?
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:   3.499
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.275
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.777
?
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
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19481938]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[28294615]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31291099]
NPO12205 Eucalyptus apodophylla Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1257 Distephanus angulifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10922 Pentaclethra macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9704 Sonneratia caseolaris Species Lythraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9319 Pterocaulon virgatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11576 Glycosmis macrophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22691 Mentha cardiaca Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6289 Ceropegia dichotoma Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9704 Sonneratia caseolaris Species Lythraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23384 Rhodiola semenovii Species Crassulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO865 Dendrobium loddigesii Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10638 Plectranthus myrianthus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3873 Crotalaria candicans Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11843 Stephania zippeliana Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12565 Hypericum polyanthemum Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11190 Veronica polita Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10922 Pentaclethra macrophylla Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5043 Eria japonica Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8934 Gypsophila perfoliata Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9532 Vernonia cistifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13135 Campylotropis hirtella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10605 Tristania conferta Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5456 Juniperus drupacea Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7773 Crinum moorei Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1257 Distephanus angulifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12796 Periploca sepium Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9319 Pterocaulon virgatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21720 Talaromyces variabilis Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7822.1 Eucalyptus globulus subsp. bicostata Subspecies Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12091 Martensia denticulata Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO526 Salvia sessei Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6731 Ononis spinosa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12205 Eucalyptus apodophylla Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1815 Breonia chinensis Species Rubiaceae 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 NPC292276 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
0.8246 Intermediate Similarity NPC183950
0.6885 Remote Similarity NPC12200
0.6667 Remote Similarity NPC120464
0.6613 Remote Similarity NPC52005
0.6562 Remote Similarity NPC605634
0.6515 Remote Similarity NPC112954
0.6491 Remote Similarity NPC50898
0.6393 Remote Similarity NPC231772
0.6393 Remote Similarity NPC62536
0.6364 Remote Similarity NPC4390
0.6349 Remote Similarity NPC606638
0.6271 Remote Similarity NPC279121
0.619 Remote Similarity NPC83508
0.6184 Remote Similarity NPC601710
0.6129 Remote Similarity NPC483773
0.6129 Remote Similarity NPC601901
0.6087 Remote Similarity NPC183
0.6 Remote Similarity NPC125062
0.6 Remote Similarity NPC279989
0.6 Remote Similarity NPC137062
0.5932 Remote Similarity NPC78540
0.5846 Remote Similarity NPC115323
0.5781 Remote Similarity NPC600900
0.5758 Remote Similarity NPC47781
0.5738 Remote Similarity NPC274121
0.5676 Remote Similarity NPC303485
0.5645 Remote Similarity NPC213216
0.5634 Remote Similarity NPC34089
0.5634 Remote Similarity NPC196179
0.561 Remote Similarity NPC113163
0.56 Remote Similarity NPC272064
0.5574 Remote Similarity NPC175013
0.5571 Remote Similarity NPC301217
0.5556 Remote Similarity NPC610974
0.5542 Remote Similarity NPC66618
0.5542 Remote Similarity NPC305987
0.5541 Remote Similarity NPC600972
0.5538 Remote Similarity NPC312924
0.5479 Remote Similarity NPC602497
0.5467 Remote Similarity NPC290830
0.5467 Remote Similarity NPC71061
0.5467 Remote Similarity NPC72425
0.5455 Remote Similarity NPC20830
0.5455 Remote Similarity NPC601565
0.5429 Remote Similarity NPC138299
0.5429 Remote Similarity NPC111112
0.5405 Remote Similarity NPC134796
0.5352 Remote Similarity NPC291746
0.5325 Remote Similarity NPC215203
0.5309 Remote Similarity NPC165970
0.5309 Remote Similarity NPC172202
0.5309 Remote Similarity NPC284127
0.5294 Remote Similarity NPC227325
0.5294 Remote Similarity NPC606105
0.5244 Remote Similarity NPC288131
0.5231 Remote Similarity NPC241498
0.5224 Remote Similarity NPC280339
0.5224 Remote Similarity NPC255350
0.5195 Remote Similarity NPC63454
0.5195 Remote Similarity NPC183851
0.5172 Remote Similarity NPC219927
0.5172 Remote Similarity NPC611172
0.5147 Remote Similarity NPC4455
0.5147 Remote Similarity NPC128863
0.5132 Remote Similarity NPC150908
0.5122 Remote Similarity NPC88023
0.5122 Remote Similarity NPC309025
0.5119 Remote Similarity NPC84324
0.5116 Remote Similarity NPC476410
0.5067 Remote Similarity NPC259757
0.5062 Remote Similarity NPC191306

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC292276 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
0.6271 Remote Similarity NPD1511 Phase 2
0.5224 Remote Similarity NPD2801 Pre-clinical

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