Structure

Physi-Chem Properties

Molecular Weight:  182.08
Volume:  165.074
LogP:  -2.143
LogD:  -2.819
LogS:  -0.141
# Rotatable Bonds:  5
TPSA:  121.38
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.261
Synthetic Accessibility Score:  3.558
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.401
MDCK Permeability:  0.00048477365635335445
Pgp-inhibitor:  0.003
Pgp-substrate:  0.784
Human Intestinal Absorption (HIA):  0.579
20% Bioavailability (F20%):  0.987
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.276
Plasma Protein Binding (PPB):  13.733040809631348%
Volume Distribution (VD):  0.332
Pgp-substrate:  76.29735565185547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.02
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.068
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.115
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.103
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  1.614
Half-life (T1/2):  0.745

ADMET: Toxicity

hERG Blockers:  0.105
Human Hepatotoxicity (H-HT):  0.028
Drug-inuced Liver Injury (DILI):  0.038
AMES Toxicity:  0.054
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.001
Skin Sensitization:  0.086
Carcinogencity:  0.004
Eye Corrosion:  0.004
Eye Irritation:  0.861
Respiratory Toxicity:  0.019

Download Data

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

  Natural Product: NPC252553

Natural Product ID:  NPC252553
Common Name*:   SWMBOMMGMHMOHE-MVNLRXSJSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SWMBOMMGMHMOHE-MVNLRXSJSA-N
Standard InCHI:  InChI=1S/2C6H14O6/c2*7-1-3(9)5(11)6(12)4(10)2-8/h2*3-12H,1-2H2/t3-,4-,5-,6-;/m1./s1
SMILES:  C([C@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O)O.C(C(C(C(C(CO)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   24848105
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002210] Sugar alcohols

*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]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. kernel n.a. PMID[10670815]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. Japan n.a. PMID[14987066]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. fruit n.a. PMID[15739361]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[15844936]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[15974623]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. Japan n.a. PMID[15974623]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits Malatya Fruit Research Institute between the first and third weeks of 2005-Jul. PMID[18038980]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. PMID[18071251]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. faeces n.a. PMID[18323202]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. seed n.a. PMID[23845552]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota seeds n.a. n.a. PMID[23999046]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. fruit n.a. PMID[240326]
NPO16230 Malus pumila Species Rosaceae Eukaryota Pericarp 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 Pollen Or Spore n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16230 Malus pumila Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24820 Taxus cuspidata Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16230 Malus pumila Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4795 Prunus armeniaca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12011 Crataegus pinnatifida Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24820 Taxus cuspidata Species Taxaceae 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 NPC252553 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 NPC252553 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