Structure

Physi-Chem Properties

Molecular Weight:  179.08
Volume:  158.724
LogP:  -2.195
LogD:  -2.165
LogS:  -0.01
# Rotatable Bonds:  1
TPSA:  116.17
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.288
Synthetic Accessibility Score:  3.844
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:  -5.383
MDCK Permeability:  0.0015128188533708453
Pgp-inhibitor:  0.002
Pgp-substrate:  0.252
Human Intestinal Absorption (HIA):  0.872
20% Bioavailability (F20%):  0.03
30% Bioavailability (F30%):  0.557

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.288
Plasma Protein Binding (PPB):  10.781015396118164%
Volume Distribution (VD):  0.381
Pgp-substrate:  90.05874633789062%

ADMET: Metabolism

CYP1A2-inhibitor:  0.018
CYP1A2-substrate:  0.038
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.339
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.087
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.172
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.034

ADMET: Excretion

Clearance (CL):  1.742
Half-life (T1/2):  0.792

ADMET: Toxicity

hERG Blockers:  0.047
Human Hepatotoxicity (H-HT):  0.246
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.334
Rat Oral Acute Toxicity:  0.122
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.462
Carcinogencity:  0.034
Eye Corrosion:  0.169
Eye Irritation:  0.225
Respiratory Toxicity:  0.175

Download Data

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

  Natural Product: NPC310601

Natural Product ID:  NPC310601
Common Name*:   MSWZFWKMSRAUBD-HOWGCPQDSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MSWZFWKMSRAUBD-HOWGCPQDSA-N
Standard InCHI:  InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6?/m0/s1
SMILES:  C([C@H]1[C@@H]([C@H]([C@@H](C(O)O1)N)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   45933887
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses

*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
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf980687v]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/JMPR.9000078]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. flower n.a. PMID[12130858]
NPO22956 Cervus nippon Species Cervidae Eukaryota n.a. n.a. n.a. PMID[15112737]
NPO1672 Apostichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. PMID[22700234]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[24211545]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[26099993]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28156114]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29400471]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[30726671]
NPO12323 Bos taurus Species Bovidae Eukaryota Urine n.a. n.a. PMID[6330305]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. PMID[932730]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. Database[FooDB]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30098 Stichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22956 Cervus nippon Species Cervidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24497 Holothuria leucospilota Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19783 Cervus elaphus Species Cervidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29632 Cervus nippon Species Cervidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24497 Holothuria leucospilota Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1672 Apostichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22956 Cervus nippon Species Cervidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19783 Cervus elaphus Species Cervidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17393 Bubalus bubalis Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30098 Stichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12323 Bos taurus Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19783 Cervus elaphus Species Cervidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22956 Cervus nippon Species Cervidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1637 Ganoderma japonicum Species Ganodermataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22258 Chrysanthemum indicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24497 Holothuria leucospilota Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1672 Apostichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4934 Phaseolus vulgaris Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12323 Bos taurus Species Bovidae 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 NPC310601 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 NPC310601 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