Structure

Physi-Chem Properties

Molecular Weight:  164.07
Volume:  147.727
LogP:  -1.26
LogD:  -1.965
LogS:  -0.248
# Rotatable Bonds:  0
TPSA:  90.15
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.326
Synthetic Accessibility Score:  3.717
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:  -5.308
MDCK Permeability:  0.0001570332096889615
Pgp-inhibitor:  0.001
Pgp-substrate:  0.94
Human Intestinal Absorption (HIA):  0.601
20% Bioavailability (F20%):  0.02
30% Bioavailability (F30%):  0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.232
Plasma Protein Binding (PPB):  14.496112823486328%
Volume Distribution (VD):  0.547
Pgp-substrate:  81.03129577636719%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.092
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.674
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.236
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.022

ADMET: Excretion

Clearance (CL):  2.468
Half-life (T1/2):  0.716

ADMET: Toxicity

hERG Blockers:  0.032
Human Hepatotoxicity (H-HT):  0.055
Drug-inuced Liver Injury (DILI):  0.192
AMES Toxicity:  0.575
Rat Oral Acute Toxicity:  0.716
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.617
Carcinogencity:  0.029
Eye Corrosion:  0.126
Eye Irritation:  0.958
Respiratory Toxicity:  0.499

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  Natural Product: NPC84938

Natural Product ID:  NPC84938
Common Name*:   SHZGCJCMOBCMKK-HGVZOGFYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SHZGCJCMOBCMKK-HGVZOGFYSA-N
Standard InCHI:  InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6+/m0/s1
SMILES:  C[C@H]1[C@@H]([C@H]([C@H]([C@H](O)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   439710
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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10075755]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11000019]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. leaves n.a. n.a. PMID[12444671]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[2026709]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota stems n.a. n.a. PMID[20387902]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. root n.a. PMID[20707067]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. rhizome n.a. PMID[20707067]
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]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
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]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25333853]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
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]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. Database[FooDB]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO31522 Fructus xanthii n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12126.1 Coix lacryma- jobi var. ma - yuen Varieties Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27403 Aralia taibaiensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24356 Fructus xanthii sibirici n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16309 Semen astragali complanati n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae 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]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29334 Oplopanax elatus Species Araliaceae 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]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8101 Rehmannia glutinosa Species Orobanchaceae 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]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9822 Typha angustifolia Species Typhaceae 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]
NPO7998 Senecio paludaffinis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5189 Glycine tomentella 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]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22666 Haematococcus lacustris Species Haematococcaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12001 Saccharomyces pastori Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21854 Pterocladiella tenuis Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27403 Aralia taibaiensis Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO731 Panax schinseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18805 Tripolium pannonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19635 Coreopsis nodosa Species Asteraceae 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 NPC84938 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 NPC84938 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