Structure

Physi-Chem Properties

Molecular Weight:  338.32
Volume:  401.376
LogP:  7.728
LogD:  4.805
LogS:  -4.574
# Rotatable Bonds:  19
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.148
Synthetic Accessibility Score:  2.147
Fsp3:  0.864
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.907
MDCK Permeability:  2.251882506243419e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.967
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.07
Plasma Protein Binding (PPB):  98.86520385742188%
Volume Distribution (VD):  3.162
Pgp-substrate:  1.089584231376648%

ADMET: Metabolism

CYP1A2-inhibitor:  0.231
CYP1A2-substrate:  0.187
CYP2C19-inhibitor:  0.374
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.15
CYP2C9-substrate:  0.939
CYP2D6-inhibitor:  0.486
CYP2D6-substrate:  0.153
CYP3A4-inhibitor:  0.53
CYP3A4-substrate:  0.069

ADMET: Excretion

Clearance (CL):  4.717
Half-life (T1/2):  0.627

ADMET: Toxicity

hERG Blockers:  0.568
Human Hepatotoxicity (H-HT):  0.027
Drug-inuced Liver Injury (DILI):  0.05
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.046
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.967
Carcinogencity:  0.083
Eye Corrosion:  0.883
Eye Irritation:  0.941
Respiratory Toxicity:  0.885

Download Data

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

  Natural Product: NPC223653

Natural Product ID:  NPC223653
Common Name*:   Pterogynine
IUPAC Name:   1,1-bis(3-methylbut-2-enyl)guanidine
Synonyms:   Pterogynine
Standard InCHIKey:  LNZWTNFGEROXJJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H21N3/c1-9(2)5-7-14(11(12)13)8-6-10(3)4/h5-6H,7-8H2,1-4H3,(H3,12,13)
SMILES:  NC(=N)N(CC=C(C)C)CC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL555502
PubChem CID:   45268797
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0000375] Guanidines

*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
NPO10824 Pterogyne nitens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19159272]
NPO10824 Pterogyne nitens Species Fabaceae Eukaryota n.a. leaf n.a. PMID[19159272]
NPO10824 Pterogyne nitens 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
NPT116 Cell Line HL-60 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[558956]
NPT180 Cell Line HCT-8 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[558956]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[558956]
NPT399 Cell Line SF-295 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[558956]

☑ 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 NPC223653 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
0.8636 High Similarity NPC188989
0.8372 Intermediate Similarity NPC253366
0.8372 Intermediate Similarity NPC97568
0.8085 Intermediate Similarity NPC32934
0.7755 Intermediate Similarity NPC153280
0.623 Remote Similarity NPC325268
0.617 Remote Similarity NPC240230
0.5893 Remote Similarity NPC39250
0.5652 Remote Similarity NPC163099
0.5625 Remote Similarity NPC270319

  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 NPC223653 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
0.6042 Remote Similarity NPD1463 Clinical (unspecified phase)
0.58 Remote Similarity NPD9458 Approved
0.5745 Remote Similarity NPD9059 Approved

  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