Structure

Physi-Chem Properties

Molecular Weight:  225.15
Volume:  232.917
LogP:  1.001
LogD:  0.169
LogS:  -2.173
# Rotatable Bonds:  5
TPSA:  87.71
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.602
Synthetic Accessibility Score:  4.043
Fsp3:  0.636
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.603
MDCK Permeability:  3.163385554216802e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.983
Human Intestinal Absorption (HIA):  0.033
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.036

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.805
Plasma Protein Binding (PPB):  49.7934684753418%
Volume Distribution (VD):  0.782
Pgp-substrate:  53.5247802734375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.03
CYP1A2-substrate:  0.072
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.136
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.516
CYP2D6-inhibitor:  0.342
CYP2D6-substrate:  0.261
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.051

ADMET: Excretion

Clearance (CL):  11.918
Half-life (T1/2):  0.588

ADMET: Toxicity

hERG Blockers:  0.042
Human Hepatotoxicity (H-HT):  0.189
Drug-inuced Liver Injury (DILI):  0.043
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.741
Maximum Recommended Daily Dose:  0.148
Skin Sensitization:  0.17
Carcinogencity:  0.118
Eye Corrosion:  0.003
Eye Irritation:  0.018
Respiratory Toxicity:  0.946

Download Data

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

  Natural Product: NPC304455

Natural Product ID:  NPC304455
Common Name*:   Plantagoguanidinic Acid
IUPAC Name:   (2R)-2-[(5R)-2-amino-4,5-dihydro-1H-imidazol-5-yl]-6-methylhept-5-enoic acid
Synonyms:  
Standard InCHIKey:  WVCALCYXKSQZFA-BDAKNGLRSA-N
Standard InCHI:  InChI=1S/C11H19N3O2/c1-7(2)4-3-5-8(10(15)16)9-6-13-11(12)14-9/h4,8-9H,3,5-6H2,1-2H3,(H,15,16)(H3,12,13,14)/t8-,9+/m1/s1
SMILES:  OC(=O)[C@@H]([C@@H]1CNC(=N)N1)CCC=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407425
PubChem CID:   71746248
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000436] Azoles
        • [CHEMONTID:0000078] Imidazoles
          • [CHEMONTID:0002310] Substituted imidazoles
            • [CHEMONTID:0001227] Imidazolyl carboxylic acids and derivatives

*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
NPO13608 Plumbago zeylanica Species Plumbaginaceae Eukaryota n.a. root n.a. PMID[16078700]
NPO13608 Plumbago zeylanica Species Plumbaginaceae Eukaryota n.a. n.a. n.a. PMID[23848163]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[26562611]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13608 Plumbago zeylanica Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13608 Plumbago zeylanica Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8918 Plantago depressa Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13608 Plumbago zeylanica Species Plumbaginaceae 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
NPT82 Cell Line MDA-MB-231 Homo sapiens IC50 > 10000.0 nM PMID[560225]
NPT461 Cell Line PANC-1 Homo sapiens IC50 > 10000.0 nM PMID[560225]
NPT984 Cell Line Hepatocyte Inhibition = 12.5 % PMID[560226]

☑ 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 NPC304455 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
0.9326 High Similarity NPC3604
0.9326 High Similarity NPC471257
0.883 High Similarity NPC471258
0.8557 High Similarity NPC471259
0.8163 Intermediate Similarity NPC471260
0.7961 Intermediate Similarity NPC147238
0.7634 Intermediate Similarity NPC304454
0.7615 Intermediate Similarity NPC471261
0.7411 Intermediate Similarity NPC471262
0.7217 Intermediate Similarity NPC471263
0.6897 Remote Similarity NPC471255
0.6765 Remote Similarity NPC40663
0.6748 Remote Similarity NPC471256
0.6531 Remote Similarity NPC90476
0.6531 Remote Similarity NPC69374
0.6222 Remote Similarity NPC133183
0.617 Remote Similarity NPC122471
0.6136 Remote Similarity NPC278881
0.6019 Remote Similarity NPC472736
0.6 Remote Similarity NPC314221
0.6 Remote Similarity NPC60424
0.5984 Remote Similarity NPC261730
0.5902 Remote Similarity NPC314293
0.5865 Remote Similarity NPC320057
0.5843 Remote Similarity NPC103130
0.5843 Remote Similarity NPC226453
0.5827 Remote Similarity NPC198644
0.5827 Remote Similarity NPC311244
0.5827 Remote Similarity NPC324722
0.5783 Remote Similarity NPC245768
0.578 Remote Similarity NPC476449
0.5745 Remote Similarity NPC328457
0.5735 Remote Similarity NPC142761
0.5729 Remote Similarity NPC327272
0.5714 Remote Similarity NPC191774
0.5714 Remote Similarity NPC193559
0.5714 Remote Similarity NPC327985
0.569 Remote Similarity NPC15413
0.5688 Remote Similarity NPC150041
0.5631 Remote Similarity NPC471867
0.5618 Remote Similarity NPC118429
0.5603 Remote Similarity NPC271562
0.5603 Remote Similarity NPC467022

  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 NPC304455 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
0.6437 Remote Similarity NPD9201 Clinical (unspecified phase)
0.6264 Remote Similarity NPD5382 Phase 2
0.618 Remote Similarity NPD9232 Phase 2
0.618 Remote Similarity NPD9231 Phase 3
0.618 Remote Similarity NPD9233 Phase 3
0.6122 Remote Similarity NPD857 Phase 3
0.6061 Remote Similarity NPD4829 Discontinued
0.5934 Remote Similarity NPD9451 Clinical (unspecified phase)
0.5893 Remote Similarity NPD6122 Discontinued
0.5859 Remote Similarity NPD3040 Approved
0.5843 Remote Similarity NPD9046 Phase 3
0.5843 Remote Similarity NPD9045 Approved
0.5843 Remote Similarity NPD9048 Approved
0.5843 Remote Similarity NPD9047 Approved
0.5746 Remote Similarity NPD6901 Phase 3
0.5714 Remote Similarity NPD4278 Clinical (unspecified phase)
0.5691 Remote Similarity NPD805 Approved
0.5691 Remote Similarity NPD806 Approved
0.5647 Remote Similarity NPD8971 Approved
0.5639 Remote Similarity NPD4153 Approved
0.5625 Remote Similarity NPD366 Approved
0.562 Remote Similarity NPD8076 Discontinued
0.5618 Remote Similarity NPD9014 Approved
0.5603 Remote Similarity NPD1829 Clinical (unspecified phase)
0.5603 Remote Similarity NPD1827 Clinical (unspecified phase)
0.5603 Remote Similarity NPD1828 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