Structure

Physi-Chem Properties

Molecular Weight:  145.16
Volume:  162.619
LogP:  -1.117
LogD:  -2.154
LogS:  0.899
# Rotatable Bonds:  7
TPSA:  64.07
# H-Bond Aceptor:  3
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.43
Synthetic Accessibility Score:  2.122
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:  -6.296
MDCK Permeability:  1.0744061000877991e-05
Pgp-inhibitor:  0.18
Pgp-substrate:  0.973
Human Intestinal Absorption (HIA):  0.11
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.19
Plasma Protein Binding (PPB):  21.103193283081055%
Volume Distribution (VD):  0.921
Pgp-substrate:  91.36402893066406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.056
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.191
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.051
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.893
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.221

ADMET: Excretion

Clearance (CL):  6.038
Half-life (T1/2):  0.309

ADMET: Toxicity

hERG Blockers:  0.049
Human Hepatotoxicity (H-HT):  0.12
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.045
Rat Oral Acute Toxicity:  0.378
Maximum Recommended Daily Dose:  0.15
Skin Sensitization:  0.94
Carcinogencity:  0.024
Eye Corrosion:  0.995
Eye Irritation:  0.074
Respiratory Toxicity:  0.769

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  Natural Product: NPC109699

Natural Product ID:  NPC109699
Common Name*:   RQFVSMCFDFGRDX-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  RQFVSMCFDFGRDX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/2C7H19N3.3H3O4P/c2*8-4-1-2-6-10-7-3-5-9;3*1-5(2,3)4/h2*10H,1-9H2;3*(H3,1,2,3,4)
SMILES:  C(CCNCCCN)CN.C(CCNCCCN)CN.OP(=O)(O)O.OP(=O)(O)O.OP(=O)(O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   39519
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0002451] Secondary amines
            • [CHEMONTID:0002228] Dialkylamines

*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
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. Wrocław, Poland 2004–2005 DOI[10.1016/J.FOODCHEM.2006.08.014]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO31303 Solanum lycopersicum Species Solanaceae 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]
NPO7635 Glycine max 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]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf950732o]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[10775096]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[11559179]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. root n.a. PMID[1622242]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16659156]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16668466]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18001808]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
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]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20954721]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[20963508]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[23479199]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds Tekirdag, Turkey PMID[24499198]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25053043]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25070365]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. PMID[25369450]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25369450]
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]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
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]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[6705789]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Cotyledon n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Hay n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Hull Husk n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Hypocotyl n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7635 Glycine max Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27009 Crotalaria retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7635 Glycine max Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7635 Glycine max Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27009 Crotalaria retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27009 Crotalaria retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7635 Glycine max Species Fabaceae 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]
NPO7635 Glycine max Species Fabaceae 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]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17694 Nicotiana tabacum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27009 Crotalaria retusa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7635 Glycine max Species Fabaceae 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 NPC109699 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 NPC109699 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