Structure

Physi-Chem Properties

Molecular Weight:  341.16
Volume:  326.069
LogP:  -1.624
LogD:  -0.46
LogS:  -0.215
# Rotatable Bonds:  8
TPSA:  152.75
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  2
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.415
Synthetic Accessibility Score:  4.627
Fsp3:  0.6
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:  -6.107
MDCK Permeability:  0.00033994155819527805
Pgp-inhibitor:  0.0
Pgp-substrate:  0.936
Human Intestinal Absorption (HIA):  0.717
20% Bioavailability (F20%):  0.165
30% Bioavailability (F30%):  0.703

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.503
Plasma Protein Binding (PPB):  34.344482421875%
Volume Distribution (VD):  0.607
Pgp-substrate:  71.76493835449219%

ADMET: Metabolism

CYP1A2-inhibitor:  0.007
CYP1A2-substrate:  0.045
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.136
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.177
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  3.783
Half-life (T1/2):  0.729

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.804
Drug-inuced Liver Injury (DILI):  0.408
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.036
Maximum Recommended Daily Dose:  0.919
Skin Sensitization:  0.163
Carcinogencity:  0.585
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.732

Download Data

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

  Natural Product: NPC471261

Natural Product ID:  NPC471261
Common Name*:   Plumbagine G
IUPAC Name:   (2R)-2-[(4R)-2-amino-1-(2,4-dihydroxybutyl)-4,5-dihydroimidazol-4-yl]-3-[(2R)-4-methyl-5-oxo-2H-furan-2-yl]propanoic acid
Synonyms:  
Standard InCHIKey:  KBSNGYTTYONWMP-YATPEIPISA-N
Standard InCHI:  InChI=1S/C15H23N3O6/c1-8-4-10(24-14(8)23)5-11(13(21)22)12-7-18(15(16)17-12)6-9(20)2-3-19/h4,9-12,19-20H,2-3,5-7H2,1H3,(H2,16,17)(H,21,22)/t9?,10-,11+,12-/m0/s1
SMILES:  OCCC(CN1C[C@H](NC1=N)[C@H](C(=O)O)C[C@H]1OC(=O)C(=C1)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407432
PubChem CID:   71746446
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]
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[544005]
NPT461 Cell Line PANC-1 Homo sapiens IC50 > 10000.0 nM PMID[544005]

☑ 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 NPC471261 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
0.9358 High Similarity NPC147238
0.8862 High Similarity NPC471256
0.8727 High Similarity NPC471259
0.8624 High Similarity NPC471258
0.8214 Intermediate Similarity NPC471260
0.8 Intermediate Similarity NPC471257
0.792 Intermediate Similarity NPC471263
0.7823 Intermediate Similarity NPC471262
0.7679 Intermediate Similarity NPC3604
0.7615 Intermediate Similarity NPC304455
0.748 Intermediate Similarity NPC471255
0.6829 Remote Similarity NPC271562
0.6822 Remote Similarity NPC235625
0.6721 Remote Similarity NPC80439
0.6721 Remote Similarity NPC279833
0.6721 Remote Similarity NPC173690
0.6715 Remote Similarity NPC261730
0.6667 Remote Similarity NPC64168
0.6585 Remote Similarity NPC6271
0.6575 Remote Similarity NPC477519
0.6565 Remote Similarity NPC106791
0.6565 Remote Similarity NPC201889
0.6555 Remote Similarity NPC150041
0.6512 Remote Similarity NPC193471
0.6512 Remote Similarity NPC130124
0.6484 Remote Similarity NPC30911
0.6484 Remote Similarity NPC316984
0.6446 Remote Similarity NPC476344
0.6439 Remote Similarity NPC174463
0.6438 Remote Similarity NPC142761
0.6357 Remote Similarity NPC168758
0.6357 Remote Similarity NPC47857
0.6357 Remote Similarity NPC181510
0.6343 Remote Similarity NPC11379
0.6336 Remote Similarity NPC103391
0.6336 Remote Similarity NPC472536
0.6331 Remote Similarity NPC311244
0.6331 Remote Similarity NPC324722
0.6331 Remote Similarity NPC198644
0.6323 Remote Similarity NPC319334
0.6323 Remote Similarity NPC327517
0.6323 Remote Similarity NPC322372
0.6316 Remote Similarity NPC284656
0.6293 Remote Similarity NPC469861
0.6293 Remote Similarity NPC130436
0.6293 Remote Similarity NPC469860
0.629 Remote Similarity NPC188785
0.6241 Remote Similarity NPC120335
0.6232 Remote Similarity NPC309525
0.6231 Remote Similarity NPC58281
0.6222 Remote Similarity NPC139867
0.6222 Remote Similarity NPC230849
0.6218 Remote Similarity NPC321485
0.6218 Remote Similarity NPC317377
0.619 Remote Similarity NPC469895
0.6183 Remote Similarity NPC76660
0.6183 Remote Similarity NPC276995
0.6176 Remote Similarity NPC315188
0.6176 Remote Similarity NPC314293
0.6148 Remote Similarity NPC40663
0.6142 Remote Similarity NPC477001
0.6142 Remote Similarity NPC477000
0.6124 Remote Similarity NPC15413
0.6119 Remote Similarity NPC209734
0.6111 Remote Similarity NPC473289
0.6102 Remote Similarity NPC304454
0.6094 Remote Similarity NPC93179
0.6084 Remote Similarity NPC133089
0.6048 Remote Similarity NPC150967
0.6043 Remote Similarity NPC36254
0.6016 Remote Similarity NPC44514
0.5986 Remote Similarity NPC469387
0.5985 Remote Similarity NPC476875
0.5969 Remote Similarity NPC236644
0.5959 Remote Similarity NPC477400
0.5957 Remote Similarity NPC145149
0.5954 Remote Similarity NPC298484
0.5942 Remote Similarity NPC23963
0.594 Remote Similarity NPC469466
0.5932 Remote Similarity NPC90476
0.5932 Remote Similarity NPC69374
0.5929 Remote Similarity NPC477985
0.5929 Remote Similarity NPC471087
0.5929 Remote Similarity NPC326386
0.5923 Remote Similarity NPC467022
0.5915 Remote Similarity NPC260270
0.5906 Remote Similarity NPC314792
0.5903 Remote Similarity NPC315011
0.5893 Remote Similarity NPC122471
0.5878 Remote Similarity NPC474099
0.5878 Remote Similarity NPC304257
0.5878 Remote Similarity NPC181086
0.587 Remote Similarity NPC314482
0.5865 Remote Similarity NPC59249
0.5859 Remote Similarity NPC475149
0.5859 Remote Similarity NPC471097
0.5857 Remote Similarity NPC323168
0.5857 Remote Similarity NPC293550
0.5857 Remote Similarity NPC477990
0.5857 Remote Similarity NPC477989
0.5857 Remote Similarity NPC111162
0.5852 Remote Similarity NPC469423
0.5833 Remote Similarity NPC477988
0.5833 Remote Similarity NPC307165
0.5827 Remote Similarity NPC245534
0.5821 Remote Similarity NPC275100
0.5821 Remote Similarity NPC478024
0.5814 Remote Similarity NPC265094
0.5814 Remote Similarity NPC68001
0.5814 Remote Similarity NPC199831
0.5814 Remote Similarity NPC474828
0.5814 Remote Similarity NPC474827
0.5809 Remote Similarity NPC473819
0.5804 Remote Similarity NPC476590
0.5804 Remote Similarity NPC471086
0.5804 Remote Similarity NPC114727
0.58 Remote Similarity NPC315848
0.58 Remote Similarity NPC315210
0.58 Remote Similarity NPC81079
0.5798 Remote Similarity NPC469363
0.5766 Remote Similarity NPC65045
0.5762 Remote Similarity NPC477401
0.5762 Remote Similarity NPC477399
0.5758 Remote Similarity NPC207820
0.5748 Remote Similarity NPC475758
0.5736 Remote Similarity NPC474244
0.5735 Remote Similarity NPC259586
0.5734 Remote Similarity NPC96010
0.5734 Remote Similarity NPC317654
0.5714 Remote Similarity NPC475975
0.5704 Remote Similarity NPC474995
0.5704 Remote Similarity NPC477518
0.5704 Remote Similarity NPC474497
0.5703 Remote Similarity NPC475791
0.5703 Remote Similarity NPC13175
0.5702 Remote Similarity NPC68819
0.5694 Remote Similarity NPC173173
0.5693 Remote Similarity NPC470621
0.5693 Remote Similarity NPC222481
0.5692 Remote Similarity NPC476877
0.5691 Remote Similarity NPC159568
0.5672 Remote Similarity NPC195435
0.5672 Remote Similarity NPC196073
0.5669 Remote Similarity NPC52820
0.5664 Remote Similarity NPC329401
0.5664 Remote Similarity NPC477987
0.5659 Remote Similarity NPC313234
0.5659 Remote Similarity NPC474873
0.5649 Remote Similarity NPC205176
0.5649 Remote Similarity NPC75523
0.563 Remote Similarity NPC40746
0.563 Remote Similarity NPC169575
0.563 Remote Similarity NPC59097
0.5629 Remote Similarity NPC473955
0.5625 Remote Similarity NPC262880
0.5625 Remote Similarity NPC475342
0.5625 Remote Similarity NPC473249
0.5625 Remote Similarity NPC247902
0.5621 Remote Similarity NPC71866
0.5621 Remote Similarity NPC304299
0.5621 Remote Similarity NPC247776
0.5621 Remote Similarity NPC475266
0.5621 Remote Similarity NPC475278
0.5621 Remote Similarity NPC309450
0.562 Remote Similarity NPC474984
0.5616 Remote Similarity NPC41162
0.5616 Remote Similarity NPC478139
0.5606 Remote Similarity NPC476876
0.5603 Remote Similarity NPC470000

  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 NPC471261 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
0.6538 Remote Similarity NPD869 Approved
0.6484 Remote Similarity NPD2204 Approved
0.6471 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6343 Remote Similarity NPD806 Approved
0.6343 Remote Similarity NPD805 Approved
0.6319 Remote Similarity NPD5767 Discontinued
0.625 Remote Similarity NPD1748 Approved
0.6222 Remote Similarity NPD2645 Approved
0.6222 Remote Similarity NPD1689 Approved
0.6194 Remote Similarity NPD1773 Discontinued
0.619 Remote Similarity NPD6122 Discontinued
0.619 Remote Similarity NPD2259 Approved
0.619 Remote Similarity NPD2258 Approved
0.6148 Remote Similarity NPD3159 Discontinued
0.6131 Remote Similarity NPD1806 Approved
0.6029 Remote Similarity NPD2132 Phase 3
0.6 Remote Similarity NPD3677 Clinical (unspecified phase)
0.5909 Remote Similarity NPD1805 Phase 2
0.5909 Remote Similarity NPD1804 Phase 2
0.5903 Remote Similarity NPD2101 Approved
0.5867 Remote Similarity NPD6077 Discontinued
0.5778 Remote Similarity NPD1376 Discontinued
0.5766 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5766 Remote Similarity NPD6935 Phase 3
0.5766 Remote Similarity NPD961 Discontinued
0.5725 Remote Similarity NPD1385 Discontinued
0.5725 Remote Similarity NPD1428 Phase 2
0.5714 Remote Similarity NPD4228 Discovery
0.5695 Remote Similarity NPD6901 Phase 3
0.5625 Remote Similarity NPD7746 Phase 1
0.5625 Remote Similarity NPD7747 Phase 1
0.56 Remote Similarity NPD4153 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