Structure

Physi-Chem Properties

Molecular Weight:  150.05
Volume:  130.431
LogP:  -2.104
LogD:  -1.857
LogS:  0.117
# 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:  0.304
Synthetic Accessibility Score:  3.803
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:  -5.257
MDCK Permeability:  0.0008067407179623842
Pgp-inhibitor:  0.001
Pgp-substrate:  0.044
Human Intestinal Absorption (HIA):  0.324
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.305

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.377
Plasma Protein Binding (PPB):  10.977177619934082%
Volume Distribution (VD):  0.441
Pgp-substrate:  83.85861206054688%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.093
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.195
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.167
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.14
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.025

ADMET: Excretion

Clearance (CL):  1.472
Half-life (T1/2):  0.735

ADMET: Toxicity

hERG Blockers:  0.053
Human Hepatotoxicity (H-HT):  0.043
Drug-inuced Liver Injury (DILI):  0.024
AMES Toxicity:  0.18
Rat Oral Acute Toxicity:  0.05
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.193
Carcinogencity:  0.047
Eye Corrosion:  0.005
Eye Irritation:  0.696
Respiratory Toxicity:  0.052

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General Info & Identifiers & Properties  
Structure MOL file  
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Similar NPs/Drugs  

  Natural Product: NPC76074

Natural Product ID:  NPC76074
Common Name*:   SRBFZHDQGSBBOR-OWMBCFKOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SRBFZHDQGSBBOR-OWMBCFKOSA-N
Standard InCHI:  InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5?/m0/s1
SMILES:  C1[C@@H]([C@@H]([C@@H](C(O)O1)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11008084
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:0001497] Pentoses

*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
NPO28778 Eucalyptus viminalis Species Myrtaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/BF00579992]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
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]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota aerial parts n.a. n.a. PMID[19299148]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
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]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. stem n.a. PMID[22210168]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22210168]
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]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[2691636]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[2691636]
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]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16741 Codonopsis pilosula Species Campanulaceae 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]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13824 Thladiantha cordifolia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28778 Eucalyptus viminalis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22659 Codonopsis subglobosa Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30421 Codonopsis tangshen Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5837 Codonopsis canescens Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO13824 Thladiantha cordifolia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5837 Codonopsis canescens Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28778 Eucalyptus viminalis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22659 Codonopsis subglobosa Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14959.1 Codonopsis pilosula subsp. tangshen Subspecies Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2865 Abrus precatorius Species Fabaceae 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]
NPO28778 Eucalyptus viminalis Species Myrtaceae 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]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO22659 Codonopsis subglobosa Species Campanulaceae 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]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13824 Thladiantha cordifolia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30421 Codonopsis tangshen Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
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]
NPO11578 Aloe vera Species Xanthorrhoeaceae 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]
NPO13291 Changium smyrnioides Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14959.1 Codonopsis pilosula subsp. tangshen Subspecies Campanulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16741 Codonopsis pilosula Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13824 Thladiantha cordifolia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5837 Codonopsis canescens Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14959.1 Codonopsis pilosula subsp. tangshen Subspecies Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28778 Eucalyptus viminalis Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22659 Codonopsis subglobosa Species Campanulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9822 Typha angustifolia Species Typhaceae 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 NPC76074 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 NPC76074 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