Structure

Physi-Chem Properties

Molecular Weight:  162.05
Volume:  145.091
LogP:  -1.914
LogD:  -1.677
LogS:  -0.028
# Rotatable Bonds:  2
TPSA:  86.99
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.396
Synthetic Accessibility Score:  3.879
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.375
MDCK Permeability:  0.0008550186757929623
Pgp-inhibitor:  0.006
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.562
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.365

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.207
Plasma Protein Binding (PPB):  27.007266998291016%
Volume Distribution (VD):  0.431
Pgp-substrate:  78.80722045898438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.019
CYP1A2-substrate:  0.064
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.122
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.094
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.119
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.053

ADMET: Excretion

Clearance (CL):  3.446
Half-life (T1/2):  0.848

ADMET: Toxicity

hERG Blockers:  0.064
Human Hepatotoxicity (H-HT):  0.032
Drug-inuced Liver Injury (DILI):  0.108
AMES Toxicity:  0.278
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.869
Carcinogencity:  0.023
Eye Corrosion:  0.39
Eye Irritation:  0.906
Respiratory Toxicity:  0.077

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC1507

Natural Product ID:  NPC1507
Common Name*:   FZRJRIPXNVGOHZ-HSUXUTPPSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  FZRJRIPXNVGOHZ-HSUXUTPPSA-N
Standard InCHI:  InChI=1S/C6H10O5/c7-1-3-5(9)6(10)4(2-8)11-3/h1,4-10H,2H2/t4-,5-,6-/m1/s1
SMILES:  C(=C1[C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   56947165
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides

*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
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. DOI[10.1021/jf970571j]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. seed n.a. PMID[10898633]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. PMID[16377847]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. PMID[20815207]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. bark n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[21319773]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[21319773]
NPO12582 Camptotheca acuminata Species Nyssaceae Eukaryota n.a. xylem n.a. PMID[21348469]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. leaf n.a. PMID[22207282]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[23806866]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. fruit n.a. PMID[240326]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO28265 Morus alba Species Moraceae Eukaryota root bark University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic 2011-APR PMID[24901948]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. Konya, Turkey 2007-APR PMID[24901948]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO28265 Morus alba Species Moraceae Eukaryota leaves Chungbuk, Korea n.a. PMID[25935644]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. root n.a. PMID[25981820]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. latex n.a. PMID[27294120]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO28265 Morus alba Species Moraceae Eukaryota Root barks n.a. n.a. PMID[3097265]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO12582 Camptotheca acuminata Species Nyssaceae Eukaryota n.a. n.a. n.a. PMID[3735324]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pollen Or Spore n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23628.1 Imperata cylindrica var. major Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30615 Fructus vitis n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10290 Fritillaria ebeiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12582 Camptotheca acuminata Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO67 Fructus mori n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO4802 Scrophularia ningpoensis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27580 Pedicellus melo n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO12582 Camptotheca acuminata Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23628.1 Imperata cylindrica var. major Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27580 Pedicellus melo n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO10226 Fructus vitis viniferae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26356 Radix vitis romanetii Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4272 Pulvis coris bovis seu bubali n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12407 Herba cichorii n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO24062 Radix pseudostellariae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4802 Scrophularia ningpoensis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15124 Herba sedi sarmentosi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO23448 Vinegar n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10290 Fritillaria ebeiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO67 Fructus mori n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO26241 Herba fragariae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4802 Scrophularia ningpoensis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12582 Camptotheca acuminata Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4802 Scrophularia ningpoensis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28265 Morus alba Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12582 Camptotheca acuminata Species Nyssaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26343 Fagopyrum esculentum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4802 Scrophularia ningpoensis Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10290 Fritillaria ebeiensis Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2746 Apis cerana Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[USDA]

☑ 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 NPC1507 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 NPC1507 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