Structure

Physi-Chem Properties

Molecular Weight:  174.11
Volume:  168.627
LogP:  -3.857
LogD:  -1.455
LogS:  -1.47
# Rotatable Bonds:  6
TPSA:  125.22
# H-Bond Aceptor:  6
# H-Bond Donor:  7
# Rings:  0
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.2
Synthetic Accessibility Score:  2.774
Fsp3:  0.667
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:  -6.474
MDCK Permeability:  0.003304604673758149
Pgp-inhibitor:  0.001
Pgp-substrate:  0.676
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.052

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.509
Plasma Protein Binding (PPB):  6.435466289520264%
Volume Distribution (VD):  0.62
Pgp-substrate:  91.96199798583984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.03
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.055
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.286
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  7.126
Half-life (T1/2):  0.636

ADMET: Toxicity

hERG Blockers:  0.075
Human Hepatotoxicity (H-HT):  0.029
Drug-inuced Liver Injury (DILI):  0.01
AMES Toxicity:  0.079
Rat Oral Acute Toxicity:  0.083
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.259
Carcinogencity:  0.045
Eye Corrosion:  0.003
Eye Irritation:  0.028
Respiratory Toxicity:  0.367

Download Data

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

  Natural Product: NPC107373

Natural Product ID:  NPC107373
Common Name*:   ODKSFYDXXFIFQN-BYPYZUCNSA-P
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  ODKSFYDXXFIFQN-BYPYZUCNSA-P
Standard InCHI:  InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+2/t4-/m0/s1
SMILES:  C(C[C@@H](C(=O)O)[NH3+])CNC(=[NH2+])N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   444360
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0002404] Alpha amino acids
                • [CHEMONTID:0004146] L-alpha-amino acids

*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
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. seed n.a. DOI[10.1007/s11418-005-0009-z]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(01)00320-X]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. leaf n.a. PMID[11738417]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. fruit n.a. PMID[21462031]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[25700090]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[32004936]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26293 Ginkgo biloba Species Ginkgoaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3107 Bupleurum falcatum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1484 Bupleurum scorzonerifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29007 Brassica juncea Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO784 Sinapis alba Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4554 Isatis tinctoria Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26293 Ginkgo biloba Species Ginkgoaceae 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 NPC107373 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 NPC107373 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