Structure

Physi-Chem Properties

Molecular Weight:  344.09
Volume:  334.655
LogP:  3.163
LogD:  2.763
LogS:  -3.955
# Rotatable Bonds:  4
TPSA:  98.36
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.751
Synthetic Accessibility Score:  2.405
Fsp3:  0.167
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.817
MDCK Permeability:  2.1830737750860862e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  88.51890563964844%
Volume Distribution (VD):  0.795
Pgp-substrate:  14.340055465698242%

ADMET: Metabolism

CYP1A2-inhibitor:  0.925
CYP1A2-substrate:  0.957
CYP2C19-inhibitor:  0.692
CYP2C19-substrate:  0.102
CYP2C9-inhibitor:  0.783
CYP2C9-substrate:  0.909
CYP2D6-inhibitor:  0.399
CYP2D6-substrate:  0.723
CYP3A4-inhibitor:  0.48
CYP3A4-substrate:  0.25

ADMET: Excretion

Clearance (CL):  4.941
Half-life (T1/2):  0.713

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.213
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.674
Rat Oral Acute Toxicity:  0.339
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.31
Carcinogencity:  0.139
Eye Corrosion:  0.004
Eye Irritation:  0.708
Respiratory Toxicity:  0.257

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General Info & Identifiers & Properties  
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Similar NPs/Drugs  

  Natural Product: NPC237156

Natural Product ID:  NPC237156
Common Name*:   RXQVMRRNRHSOTC-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RXQVMRRNRHSOTC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H16O7/c1-22-10-6-4-9(5-7-10)15-18(24-3)14(21)13-11(19)8-12(20)16(23-2)17(13)25-15/h4-8,19-20H,1-3H3
SMILES:  COc1ccc(cc1)c1c(c(=O)c2c(cc(c(c2o1)OC)O)O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   13916278
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002593] 8-O-methylated flavonoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO25128 Panax vietnamensis Species Araliaceae Eukaryota n.a. Vietnamese n.a. PMID[11325227]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[12542368]
NPO25088 Larrea tridentata Species Zygophyllaceae Eukaryota n.a. n.a. n.a. PMID[12960376]
NPO22637 Kunzea ambigua Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[15043420]
NPO10407 Petromyzon marinus Species Petromyzontidae Eukaryota n.a. n.a. n.a. PMID[15193266]
NPO140 Coriaria japonica Species Coriariaceae Eukaryota n.a. fruit n.a. PMID[16079545]
NPO3544 Sophora mollis Species Fabaceae Eukaryota roots n.a. n.a. PMID[19572738]
NPO6431 Strophioblachia fimbricalyx Species Euphorbiaceae Eukaryota roots n.a. n.a. PMID[19778068]
NPO25088 Larrea tridentata Species Zygophyllaceae Eukaryota n.a. n.a. n.a. PMID[2166136]
NPO27656 Lotus edulis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22014228]
NPO27656 Lotus edulis Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22014228]
NPO27656 Lotus edulis Species Fabaceae Eukaryota n.a. branch n.a. PMID[22014228]
NPO6431 Strophioblachia fimbricalyx Species Euphorbiaceae Eukaryota Roots n.a. n.a. PMID[23806014]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[28139925]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[31184894]
NPO140 Coriaria japonica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25088 Larrea tridentata Species Zygophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24672 Helleborus purpurascens Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO140 Coriaria japonica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4794 Conyza stricta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24672 Helleborus purpurascens Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25088 Larrea tridentata Species Zygophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO140 Coriaria japonica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25557 Alternaria porri Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24866 Smilax aspera Species Smilacaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8326 Brunsvigia cooperi Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4546 Evodiella muelleri Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24549 Scutellaria cordifrons Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18646 Rubus rosifolius Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25088 Larrea tridentata Species Zygophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25410 Manilkara bidentata Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5574 Schelhammera undulata Species Colchicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24672 Helleborus purpurascens Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6431 Strophioblachia fimbricalyx Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27656 Lotus edulis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1679 Plagiogyria dunnii Species Plagiogyriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO65 Geranium palustre Species Geraniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5676 Annulohypoxylon multiforme Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6156 Impatiens pallida Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24735 Cupania latifolia Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28771 Clematis delavayi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2674 Bidens leucanthus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO140 Coriaria japonica Species Coriariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16885 Phonus arborescens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24821 Nidorella resedifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3544 Sophora mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO257 Aplophyllum griffithianum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4794 Conyza stricta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8551 Trididemnum inarmatum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25468 Tabernaemontana amygdalifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25128 Panax vietnamensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6344 Rutidosis murchisonii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO700 Cassia multijuga Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19721 Impatiens roylei Species Balsaminaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24591 Trichosanthes dioica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6100 Senecio pleistocephalus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17249 Lespedeza capitata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2394 Myoporum tenuifolium Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23489 Stachys anisochila Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5245 Angiopteris palmiformis Species Marattiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22637 Kunzea ambigua Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8943 Juniperus californica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10407 Petromyzon marinus Species Petromyzontidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25321 Acantholimon glumaceum Species Plumbaginaceae 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 NP ID 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1048 Organism Poliovirus Human enterovirus C Max non-toxic dose > 10.0 ug ml-1 PMID[487496]
NPT1048 Organism Poliovirus Human enterovirus C Reduction factor = 1.0 n.a. PMID[487496]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC237156 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC237156 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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