Structure

Physi-Chem Properties

Molecular Weight:  195.17
Volume:  223.893
LogP:  2.854
LogD:  1.619
LogS:  -2.444
# Rotatable Bonds:  5
TPSA:  50.41
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.408
Synthetic Accessibility Score:  3.251
Fsp3:  0.545
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:  -4.905
MDCK Permeability:  7.191297299868893e-06
Pgp-inhibitor:  0.272
Pgp-substrate:  0.991
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.868
30% Bioavailability (F30%):  0.048

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.8
Plasma Protein Binding (PPB):  84.42359924316406%
Volume Distribution (VD):  3.468
Pgp-substrate:  18.444833755493164%

ADMET: Metabolism

CYP1A2-inhibitor:  0.267
CYP1A2-substrate:  0.095
CYP2C19-inhibitor:  0.034
CYP2C19-substrate:  0.399
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.145
CYP2D6-inhibitor:  0.762
CYP2D6-substrate:  0.822
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.203

ADMET: Excretion

Clearance (CL):  16.891
Half-life (T1/2):  0.345

ADMET: Toxicity

hERG Blockers:  0.1
Human Hepatotoxicity (H-HT):  0.928
Drug-inuced Liver Injury (DILI):  0.018
AMES Toxicity:  0.038
Rat Oral Acute Toxicity:  0.863
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.396
Carcinogencity:  0.08
Eye Corrosion:  0.003
Eye Irritation:  0.023
Respiratory Toxicity:  0.953

Download Data

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

  Natural Product: NPC188989

Natural Product ID:  NPC188989
Common Name*:   Pterogynidine
IUPAC Name:   1,2-bis(3-methylbut-2-enyl)guanidine
Synonyms:   Pterogynidine
Standard InCHIKey:  PDIPOEDZYMYFGI-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H21N3/c1-9(2)5-7-13-11(12)14-8-6-10(3)4/h5-6H,7-8H2,1-4H3,(H3,12,13,14)/p+1
SMILES:  CC(=CCNC(=[NH2+])NCC=C(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509539
PubChem CID:   10035557
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[478640]
NPT180 Cell Line HCT-8 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[478640]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[478640]
NPT399 Cell Line SF-295 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[478640]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IC12 = 8.5 ug ml-1 PMID[478639]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IC12 > 1000.0 ug ml-1 PMID[478639]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 4.0 ug.mL-1 PMID[478641]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MBC99.9 = 4.0 mg/ml PMID[478641]

☑ 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 NPC188989 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
0.9333 High Similarity NPC32934
0.9286 High Similarity NPC253366
0.9286 High Similarity NPC97568
0.8636 High Similarity NPC223653
0.8542 High Similarity NPC153280
0.7119 Intermediate Similarity NPC325268
0.6852 Remote Similarity NPC39250
0.6596 Remote Similarity NPC240230
0.6444 Remote Similarity NPC163099
0.6383 Remote Similarity NPC270319
0.6296 Remote Similarity NPC230087

  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 NPC188989 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
0.6889 Remote Similarity NPD9059 Approved
0.6875 Remote Similarity NPD9458 Approved
0.6458 Remote Similarity NPD1463 Clinical (unspecified phase)
0.6122 Remote Similarity NPD9015 Phase 2
0.5962 Remote Similarity NPD9674 Approved
0.5962 Remote Similarity NPD9675 Approved
0.5652 Remote Similarity NPD1144 Phase 2

  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