Structure

Physi-Chem Properties

Molecular Weight:  243.16
Volume:  244.344
LogP:  -1.242
LogD:  -0.535
LogS:  -1.173
# Rotatable Bonds:  6
TPSA:  107.94
# H-Bond Aceptor:  6
# H-Bond Donor:  5
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.521
Synthetic Accessibility Score:  4.007
Fsp3:  0.818
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:  -5.884
MDCK Permeability:  0.0004846605588681996
Pgp-inhibitor:  0.002
Pgp-substrate:  0.862
Human Intestinal Absorption (HIA):  0.053
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.664
Plasma Protein Binding (PPB):  23.236101150512695%
Volume Distribution (VD):  0.524
Pgp-substrate:  78.94770050048828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.009
CYP1A2-substrate:  0.068
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.075
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.526
CYP2D6-inhibitor:  0.073
CYP2D6-substrate:  0.262
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.052

ADMET: Excretion

Clearance (CL):  7.196
Half-life (T1/2):  0.536

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.05
Drug-inuced Liver Injury (DILI):  0.06
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.088
Maximum Recommended Daily Dose:  0.161
Skin Sensitization:  0.103
Carcinogencity:  0.116
Eye Corrosion:  0.003
Eye Irritation:  0.022
Respiratory Toxicity:  0.927

Download Data

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

  Natural Product: NPC304454

Natural Product ID:  NPC304454
Common Name*:   (2R,4'r)-Plantagoamidinic Acid B
IUPAC Name:   (2R)-2-[(5R)-2-amino-4,5-dihydro-1H-imidazol-5-yl]-6-hydroxy-6-methylheptanoic acid
Synonyms:  
Standard InCHIKey:  GBSCWVANWSJNOB-SFYZADRCSA-N
Standard InCHI:  InChI=1S/C11H21N3O3/c1-11(2,17)5-3-4-7(9(15)16)8-6-13-10(12)14-8/h7-8,17H,3-6H2,1-2H3,(H,15,16)(H3,12,13,14)/t7-,8+/m1/s1
SMILES:  OC(=O)[C@@H]([C@@H]1CNC(=N)N1)CCCC(O)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407424
PubChem CID:   71746629
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0000299] Medium-chain hydroxy 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]
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]
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[538441]
NPT461 Cell Line PANC-1 Homo sapiens IC50 > 10000.0 nM PMID[538441]

☑ 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 NPC304454 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
0.7634 Intermediate Similarity NPC304455
0.7273 Intermediate Similarity NPC472736
0.7172 Intermediate Similarity NPC471257
0.7172 Intermediate Similarity NPC3604
0.699 Remote Similarity NPC471258
0.6792 Remote Similarity NPC471259
0.6667 Remote Similarity NPC278881
0.6458 Remote Similarity NPC199072
0.6455 Remote Similarity NPC469388
0.6455 Remote Similarity NPC469389
0.6455 Remote Similarity NPC472737
0.6449 Remote Similarity NPC471260
0.6364 Remote Similarity NPC133183
0.6339 Remote Similarity NPC147238
0.6118 Remote Similarity NPC302188
0.6116 Remote Similarity NPC477518
0.6102 Remote Similarity NPC471261
0.6061 Remote Similarity NPC277918
0.6 Remote Similarity NPC15864
0.5977 Remote Similarity NPC226453
0.5977 Remote Similarity NPC103130
0.5952 Remote Similarity NPC319279
0.595 Remote Similarity NPC471262
0.5929 Remote Similarity NPC15413
0.5926 Remote Similarity NPC245768
0.587 Remote Similarity NPC328457
0.5851 Remote Similarity NPC327272
0.5843 Remote Similarity NPC327985
0.5842 Remote Similarity NPC469363
0.5833 Remote Similarity NPC191774
0.5833 Remote Similarity NPC278209
0.5806 Remote Similarity NPC471263
0.5795 Remote Similarity NPC57420
0.5747 Remote Similarity NPC118429
0.5703 Remote Similarity NPC261730
0.5686 Remote Similarity NPC90476
0.5686 Remote Similarity NPC69374
0.5679 Remote Similarity NPC50457
0.5673 Remote Similarity NPC203170
0.5673 Remote Similarity NPC322966
0.567 Remote Similarity NPC233108
0.5669 Remote Similarity NPC311244
0.5669 Remote Similarity NPC324722
0.5669 Remote Similarity NPC198644
0.5667 Remote Similarity NPC325534
0.5667 Remote Similarity NPC470108
0.5632 Remote Similarity NPC327170
0.5632 Remote Similarity NPC329564
0.5614 Remote Similarity NPC236644
0.561 Remote Similarity NPC202525
0.5604 Remote Similarity NPC470109

  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 NPC304454 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
0.7048 Intermediate Similarity NPD1827 Clinical (unspecified phase)
0.7048 Intermediate Similarity NPD1828 Approved
0.7048 Intermediate Similarity NPD1829 Clinical (unspecified phase)
0.7037 Intermediate Similarity NPD9676 Phase 3
0.6813 Remote Similarity NPD617 Approved
0.6782 Remote Similarity NPD5382 Phase 2
0.6458 Remote Similarity NPD326 Approved
0.6437 Remote Similarity NPD9451 Clinical (unspecified phase)
0.6381 Remote Similarity NPD4825 Clinical (unspecified phase)
0.6354 Remote Similarity NPD4829 Discontinued
0.6337 Remote Similarity NPD2682 Approved
0.6322 Remote Similarity NPD9233 Phase 3
0.6322 Remote Similarity NPD9231 Phase 3
0.6322 Remote Similarity NPD9232 Phase 2
0.6322 Remote Similarity NPD375 Phase 2
0.6296 Remote Similarity NPD9454 Approved
0.6273 Remote Similarity NPD8175 Discontinued
0.6147 Remote Similarity NPD6122 Discontinued
0.6118 Remote Similarity NPD9656 Approved
0.6019 Remote Similarity NPD5359 Clinical (unspecified phase)
0.5982 Remote Similarity NPD6937 Approved
0.5981 Remote Similarity NPD3713 Approved
0.5981 Remote Similarity NPD3714 Approved
0.5981 Remote Similarity NPD3715 Approved
0.5977 Remote Similarity NPD9048 Approved
0.5977 Remote Similarity NPD9046 Phase 3
0.5977 Remote Similarity NPD9045 Approved
0.5977 Remote Similarity NPD9047 Approved
0.5962 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5955 Remote Similarity NPD9421 Phase 1
0.5952 Remote Similarity NPD9439 Approved
0.5952 Remote Similarity NPD9438 Approved
0.5941 Remote Similarity NPD3176 Clinical (unspecified phase)
0.5849 Remote Similarity NPD573 Clinical (unspecified phase)
0.5841 Remote Similarity NPD1126 Phase 2
0.5833 Remote Similarity NPD4278 Clinical (unspecified phase)
0.5806 Remote Similarity NPD1147 Phase 2
0.578 Remote Similarity NPD3101 Approved
0.578 Remote Similarity NPD3102 Approved
0.578 Remote Similarity NPD3103 Approved
0.578 Remote Similarity NPD3104 Approved
0.5747 Remote Similarity NPD9014 Approved
0.5745 Remote Similarity NPD366 Approved
0.5728 Remote Similarity NPD621 Discontinued
0.5684 Remote Similarity NPD632 Discontinued
0.5667 Remote Similarity NPD8952 Approved
0.5652 Remote Similarity NPD620 Approved
0.5638 Remote Similarity NPD6944 Clinical (unspecified phase)
0.56 Remote Similarity NPD1125 Discovery
0.56 Remote Similarity NPD857 Phase 3

  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