Structure

Physi-Chem Properties

Molecular Weight:  328.12
Volume:  310.659
LogP:  -0.357
LogD:  -0.27
LogS:  -1.376
# Rotatable Bonds:  5
TPSA:  125.68
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.511
Synthetic Accessibility Score:  3.358
Fsp3:  0.533
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.702
MDCK Permeability:  4.629692557500675e-05
Pgp-inhibitor:  0.018
Pgp-substrate:  0.089
Human Intestinal Absorption (HIA):  0.723
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.836

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.431
Plasma Protein Binding (PPB):  35.51189422607422%
Volume Distribution (VD):  0.39
Pgp-substrate:  43.284332275390625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.096
CYP1A2-substrate:  0.21
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.67
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.339
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.304
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.07

ADMET: Excretion

Clearance (CL):  2.521
Half-life (T1/2):  0.788

ADMET: Toxicity

hERG Blockers:  0.182
Human Hepatotoxicity (H-HT):  0.047
Drug-inuced Liver Injury (DILI):  0.504
AMES Toxicity:  0.179
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.067
Carcinogencity:  0.061
Eye Corrosion:  0.004
Eye Irritation:  0.131
Respiratory Toxicity:  0.015

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  Natural Product: NPC111625

Natural Product ID:  NPC111625
Common Name*:   QUOZWMJFTQUXON-UXXRCYHCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QUOZWMJFTQUXON-UXXRCYHCSA-N
Standard InCHI:  InChI=1S/C15H20O8/c1-7(17)8-3-4-9(10(5-8)21-2)22-15-14(20)13(19)12(18)11(6-16)23-15/h3-5,11-16,18-20H,6H2,1-2H3/t11-,12-,13+,14-,15-/m1/s1
SMILES:  CC(=O)c1ccc(c(c1)OC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   164648
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

*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
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[10075762]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[18636777]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota fresh stems n.a. n.a. PMID[20159656]
NPO7528 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[21465599]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[24433009]
NPO7528 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[25036154]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. PMID[28006909]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. PMID[28032759]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO284 Albizia procera Species Fabaceae Eukaryota Bark n.a. n.a. PMID[30520635]
NPO7528 Belamcanda chinensis Species Iridaceae Eukaryota Rhizomes n.a. n.a. PMID[31246464]
NPO40254 Opuntia humifusa Species Cactaceae Eukaryota Cladodes n.a. n.a. PMID[32118424]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20990 Garcinia ovalifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21188 Merremia quinquefolia Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20990 Garcinia ovalifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7528 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1757 Aconitum liljestrandii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7528 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6964 Cistanche tubulosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3263 Thea sasanqua n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17969 Unona lawii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27620 Pteris cretica Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7464 Uruparia lanosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20990 Garcinia ovalifolia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2963 Diospyros glaucifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1757 Aconitum liljestrandii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19591 Dendrocalamus strictus Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20302 Betonica grandiflora Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4117 Nauclea rhynchophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14417 Iris tectorum Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7528 Belamcanda chinensis Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15597 Calystegia pubescens Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10092 Hesperocyparis bakeri Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21188 Merremia quinquefolia Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3093 Phyllanthus tenellus Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8416 Picrorhiza kurrooa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4952 Pertusaria amara Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29287 Alectoria ochroleuca Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19951 Parmelia amphixanthoides Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20531 Helichrysum splendidum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21261 Funtumia africana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14720 Neopicrorhiza scrophulariiflora Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7616 Melanargia galathea Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO855 Elymnias thryallis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6844 Bulbophyllum protractum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14818 Neofusicoccum mangiferae Species Botryosphaeriaceae 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

☑ 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 NPC111625 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 NPC111625 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