Structure

Physi-Chem Properties

Molecular Weight:  180.06
Volume:  162.437
LogP:  -2.184
LogD:  -2.4
LogS:  0.129
# Rotatable Bonds:  5
TPSA:  118.22
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.301
Synthetic Accessibility Score:  3.801
Fsp3:  0.833
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:  -5.317
MDCK Permeability:  0.002156463684514165
Pgp-inhibitor:  0.016
Pgp-substrate:  0.065
Human Intestinal Absorption (HIA):  0.08
20% Bioavailability (F20%):  0.887
30% Bioavailability (F30%):  0.862

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.6
Plasma Protein Binding (PPB):  13.487197875976562%
Volume Distribution (VD):  0.737
Pgp-substrate:  76.8724594116211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.03
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.054
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.077
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.101
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.013

ADMET: Excretion

Clearance (CL):  1.401
Half-life (T1/2):  0.839

ADMET: Toxicity

hERG Blockers:  0.069
Human Hepatotoxicity (H-HT):  0.183
Drug-inuced Liver Injury (DILI):  0.865
AMES Toxicity:  0.055
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.134
Carcinogencity:  0.003
Eye Corrosion:  0.004
Eye Irritation:  0.1
Respiratory Toxicity:  0.02

Download Data

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

  Natural Product: NPC113101

Natural Product ID:  NPC113101
Common Name*:   BJHIKXHVCXFQLS-UYFOZJQFSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BJHIKXHVCXFQLS-UYFOZJQFSA-N
Standard InCHI:  InChI=1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h3,5-9,11-12H,1-2H2/t3-,5-,6-/m1/s1
SMILES:  C([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5984
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
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[15678383]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[16045947]
NPO8764 Laurencia decumbens Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[17711344]
NPO8653 Leuconostoc mesenteroides Species Leuconostocaceae Bacteria n.a. n.a. n.a. PMID[19025748]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. PMID[19245240]
NPO25696 Hyptis brevipes Species Lamiaceae Eukaryota Whole Plant Tawangmangu village, Karanganyar, Central Java, Indonesia 2003-FEB PMID[19422206]
NPO25696 Hyptis brevipes Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[19422206]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. stem n.a. PMID[20188156]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. PMID[20581114]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[22351977]
NPO25696 Hyptis brevipes Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23282042]
NPO17878 Ips paraconfusus Species Curculionidae Eukaryota n.a. n.a. n.a. PMID[24318848]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. PMID[25515814]
NPO25696 Hyptis brevipes Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[28099005]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. Malaysian n.a. PMID[7506311]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO26622 Taraxacum officinale Species Asteraceae 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 Plant n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28741 Afrocarpus gracilior Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18407 Pteris fauriei Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17266 Hedychium yunnanense Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12468 Asarum heterotropoides Species Aristolochiaceae 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]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13668 Taraxacum platycarpum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23327 Taraxacum coreanum Species Asteraceae 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]
NPO1596 Taraxacum borealisinense Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9136 Pseudocyclosorus subochthodes Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26103 Streptomyces bobili Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO4011 Chlamydomonas reinhardtii Species Chlamydomonadaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18446 Paradendryphiella salina Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26785 Taraxacum mongolicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13668 Taraxacum platycarpum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12468 Asarum heterotropoides Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6766 Antiphiona pinnatisecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23327 Taraxacum coreanum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9567 Enicosanthum cupulare Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14138 Centaurea aspera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8653 Leuconostoc mesenteroides Species Leuconostocaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17878 Ips paraconfusus Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26622 Taraxacum officinale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24671 Lycopodium japonicum Species Lycopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19816 Crotalaria novae-hollandiae Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28741 Afrocarpus gracilior Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2804 Calophyllum inophyllum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3123 Anthemis cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10991 Maackia tashiroi Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18407 Pteris fauriei Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2495 Agave xylonacantha Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19826 Helicoverpa armigera Species 0ctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2012 Turnera diffusa Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17266 Hedychium yunnanense Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25696 Hyptis brevipes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8764 Laurencia decumbens Species Rhodomelaceae 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
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[528851]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[528851]

☑ 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 NPC113101 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 NPC113101 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