Structure

Physi-Chem Properties

Molecular Weight:  473.2
Volume:  439.154
LogP:  -2.069
LogD:  -1.137
LogS:  -0.524
# Rotatable Bonds:  10
TPSA:  211.67
# H-Bond Aceptor:  13
# H-Bond Donor:  8
# Rings:  3
# Heavy Atoms:  13

MedChem Properties

QED Drug-Likeness Score:  0.192
Synthetic Accessibility Score:  5.149
Fsp3:  0.7
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
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:  -6.323
MDCK Permeability:  7.152908074203879e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.918
20% Bioavailability (F20%):  0.843
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.363
Plasma Protein Binding (PPB):  40.545223236083984%
Volume Distribution (VD):  0.293
Pgp-substrate:  61.56148147583008%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.028
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.048
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.068
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.137
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.002

ADMET: Excretion

Clearance (CL):  1.164
Half-life (T1/2):  0.711

ADMET: Toxicity

hERG Blockers:  0.065
Human Hepatotoxicity (H-HT):  0.59
Drug-inuced Liver Injury (DILI):  0.703
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.909
Skin Sensitization:  0.104
Carcinogencity:  0.095
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.609

Download Data

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

  Natural Product: NPC471256

Natural Product ID:  NPC471256
Common Name*:   Plumbagine G Alpha-D-Xyloside
IUPAC Name:   (2R)-2-[(4R)-2-amino-1-[2-hydroxy-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxybutyl]-4,5-dihydroimidazol-4-yl]-3-[(2R)-4-methyl-5-oxo-2H-furan-2-yl]propanoic acid
Synonyms:  
Standard InCHIKey:  GSQGGVXWVLMSPQ-MDYKANHUSA-N
Standard InCHI:  InChI=1S/C20H31N3O10/c1-9-4-11(33-18(9)30)5-12(17(28)29)13-7-23(20(21)22-13)6-10(24)2-3-31-19-16(27)15(26)14(25)8-32-19/h4,10-16,19,24-27H,2-3,5-8H2,1H3,(H2,21,22)(H,28,29)/t10?,11-,12+,13-,14+,15-,16+,19-/m0/s1
SMILES:  OC(CN1C[C@H](NC1=N)[C@H](C(=O)O)C[C@H]1OC(=O)C(=C1)C)CCO[C@H]1OC[C@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407423
PubChem CID:   71746628
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002207] O-glycosyl compounds

*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[459685]
NPT461 Cell Line PANC-1 Homo sapiens IC50 > 10000.0 nM PMID[459685]

☑ 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 NPC471256 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
0.904 High Similarity NPC471263
0.8952 High Similarity NPC471262
0.8862 High Similarity NPC471261
0.8583 High Similarity NPC471255
0.8293 Intermediate Similarity NPC147238
0.7742 Intermediate Similarity NPC471259
0.7642 Intermediate Similarity NPC471258
0.7302 Intermediate Similarity NPC471260
0.7097 Intermediate Similarity NPC471257
0.6861 Remote Similarity NPC235625
0.6825 Remote Similarity NPC3604
0.6748 Remote Similarity NPC304455
0.6687 Remote Similarity NPC327517
0.6687 Remote Similarity NPC319334
0.6687 Remote Similarity NPC322372
0.6619 Remote Similarity NPC201889
0.6619 Remote Similarity NPC106791
0.6584 Remote Similarity NPC317377
0.6584 Remote Similarity NPC321485
0.6569 Remote Similarity NPC193471
0.6569 Remote Similarity NPC130124
0.6544 Remote Similarity NPC316984
0.6544 Remote Similarity NPC30911
0.6536 Remote Similarity NPC247776
0.6536 Remote Similarity NPC71866
0.6536 Remote Similarity NPC309450
0.6536 Remote Similarity NPC475278
0.6536 Remote Similarity NPC304299
0.6536 Remote Similarity NPC475266
0.6525 Remote Similarity NPC314482
0.6466 Remote Similarity NPC64168
0.646 Remote Similarity NPC477398
0.6458 Remote Similarity NPC477985
0.6458 Remote Similarity NPC326386
0.6458 Remote Similarity NPC471087
0.6423 Remote Similarity NPC47857
0.6423 Remote Similarity NPC181510
0.6423 Remote Similarity NPC168758
0.6419 Remote Similarity NPC261730
0.6391 Remote Similarity NPC80439
0.6391 Remote Similarity NPC279833
0.6391 Remote Similarity NPC6271
0.6391 Remote Similarity NPC173690
0.6389 Remote Similarity NPC477990
0.6389 Remote Similarity NPC111162
0.6389 Remote Similarity NPC318445
0.6389 Remote Similarity NPC293550
0.6389 Remote Similarity NPC323168
0.6389 Remote Similarity NPC316133
0.6389 Remote Similarity NPC477989
0.6383 Remote Similarity NPC284656
0.6351 Remote Similarity NPC477988
0.6327 Remote Similarity NPC471086
0.6312 Remote Similarity NPC6531
0.6312 Remote Similarity NPC65045
0.6306 Remote Similarity NPC477519
0.6299 Remote Similarity NPC315210
0.6299 Remote Similarity NPC315848
0.6286 Remote Similarity NPC472536
0.6286 Remote Similarity NPC103391
0.6276 Remote Similarity NPC315783
0.6268 Remote Similarity NPC174463
0.6259 Remote Similarity NPC1111
0.6259 Remote Similarity NPC261750
0.625 Remote Similarity NPC271562
0.6241 Remote Similarity NPC30196
0.6233 Remote Similarity NPC36254
0.6216 Remote Similarity NPC173173
0.62 Remote Similarity NPC316401
0.619 Remote Similarity NPC329401
0.619 Remote Similarity NPC477987
0.6181 Remote Similarity NPC230849
0.6178 Remote Similarity NPC142761
0.617 Remote Similarity NPC259586
0.6164 Remote Similarity NPC314629
0.6143 Remote Similarity NPC60432
0.6138 Remote Similarity NPC470000
0.6127 Remote Similarity NPC470621
0.6127 Remote Similarity NPC222481
0.6111 Remote Similarity NPC138534
0.6111 Remote Similarity NPC314268
0.6111 Remote Similarity NPC313802
0.6111 Remote Similarity NPC67917
0.6111 Remote Similarity NPC477986
0.6111 Remote Similarity NPC477515
0.6096 Remote Similarity NPC94319
0.6096 Remote Similarity NPC20035
0.6093 Remote Similarity NPC120335
0.6081 Remote Similarity NPC309525
0.6071 Remote Similarity NPC58281
0.6069 Remote Similarity NPC11379
0.6067 Remote Similarity NPC324722
0.6067 Remote Similarity NPC198644
0.6067 Remote Similarity NPC311244
0.6061 Remote Similarity NPC306041
0.6058 Remote Similarity NPC475918
0.604 Remote Similarity NPC314282
0.6029 Remote Similarity NPC55336
0.6028 Remote Similarity NPC43648
0.6028 Remote Similarity NPC478024
0.6027 Remote Similarity NPC315188
0.6027 Remote Similarity NPC23963
0.6024 Remote Similarity NPC316244
0.6014 Remote Similarity NPC315426
0.6 Remote Similarity NPC57436
0.6 Remote Similarity NPC163783
0.6 Remote Similarity NPC9447
0.6 Remote Similarity NPC121479
0.5987 Remote Similarity NPC315011
0.5985 Remote Similarity NPC150041
0.596 Remote Similarity NPC316205
0.596 Remote Similarity NPC315387
0.5959 Remote Similarity NPC139867
0.5956 Remote Similarity NPC261117
0.5956 Remote Similarity NPC310804
0.5948 Remote Similarity NPC314361
0.5948 Remote Similarity NPC133089
0.5935 Remote Similarity NPC477400
0.5935 Remote Similarity NPC297058
0.5933 Remote Similarity NPC473249
0.5918 Remote Similarity NPC314293
0.5915 Remote Similarity NPC76660
0.5915 Remote Similarity NPC276995
0.5915 Remote Similarity NPC275100
0.5915 Remote Similarity NPC314306
0.5906 Remote Similarity NPC314512
0.5906 Remote Similarity NPC313333
0.5906 Remote Similarity NPC313342
0.5906 Remote Similarity NPC469999
0.5906 Remote Similarity NPC314451
0.5896 Remote Similarity NPC150967
0.5896 Remote Similarity NPC476344
0.587 Remote Similarity NPC477001
0.587 Remote Similarity NPC477000
0.5862 Remote Similarity NPC469997
0.5862 Remote Similarity NPC209734
0.5852 Remote Similarity NPC470094
0.5849 Remote Similarity NPC477399
0.5849 Remote Similarity NPC477401
0.5839 Remote Similarity NPC250545
0.5839 Remote Similarity NPC325750
0.5827 Remote Similarity NPC266718
0.5821 Remote Similarity NPC54731
0.5811 Remote Similarity NPC245534
0.5804 Remote Similarity NPC474497
0.5804 Remote Similarity NPC474995
0.5802 Remote Similarity NPC6414
0.5802 Remote Similarity NPC303451
0.5802 Remote Similarity NPC118078
0.5797 Remote Similarity NPC469895
0.5789 Remote Similarity NPC260270
0.5786 Remote Similarity NPC254538
0.5786 Remote Similarity NPC474285
0.5783 Remote Similarity NPC265699
0.5781 Remote Similarity NPC469363
0.578 Remote Similarity NPC473040
0.5775 Remote Similarity NPC196073
0.5775 Remote Similarity NPC195435
0.5766 Remote Similarity NPC298255
0.5766 Remote Similarity NPC188785
0.5766 Remote Similarity NPC28304
0.5764 Remote Similarity NPC241597
0.5764 Remote Similarity NPC475988
0.5762 Remote Similarity NPC315058
0.5762 Remote Similarity NPC474371
0.5759 Remote Similarity NPC181086
0.5755 Remote Similarity NPC86095
0.5749 Remote Similarity NPC113620
0.5749 Remote Similarity NPC174336
0.5749 Remote Similarity NPC187497
0.5749 Remote Similarity NPC475599
0.5749 Remote Similarity NPC100612
0.5745 Remote Similarity NPC474099
0.5736 Remote Similarity NPC130436
0.5736 Remote Similarity NPC469860
0.5736 Remote Similarity NPC469861
0.5725 Remote Similarity NPC473289
0.5724 Remote Similarity NPC145149
0.5724 Remote Similarity NPC474984
0.5714 Remote Similarity NPC61201
0.5714 Remote Similarity NPC236644
0.5714 Remote Similarity NPC472195
0.5714 Remote Similarity NPC472196
0.5714 Remote Similarity NPC238090
0.5714 Remote Similarity NPC307165
0.5714 Remote Similarity NPC93179
0.5704 Remote Similarity NPC298484
0.5703 Remote Similarity NPC475035
0.5696 Remote Similarity NPC230889
0.5694 Remote Similarity NPC469466
0.5694 Remote Similarity NPC279383
0.5693 Remote Similarity NPC255677
0.5693 Remote Similarity NPC22149
0.5693 Remote Similarity NPC306344
0.5692 Remote Similarity NPC475037
0.5689 Remote Similarity NPC475527
0.5687 Remote Similarity NPC81079
0.5686 Remote Similarity NPC329919
0.5686 Remote Similarity NPC477793
0.5683 Remote Similarity NPC474827

  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 NPC471256 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
0.6544 Remote Similarity NPD2204 Approved
0.6528 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6389 Remote Similarity NPD7642 Approved
0.6383 Remote Similarity NPD7641 Discontinued
0.6357 Remote Similarity NPD869 Approved
0.6276 Remote Similarity NPD7829 Approved
0.6276 Remote Similarity NPD7830 Approved
0.6133 Remote Similarity NPD8391 Approved
0.6133 Remote Similarity NPD8390 Approved
0.6133 Remote Similarity NPD8392 Approved
0.6096 Remote Similarity NPD4826 Approved
0.6096 Remote Similarity NPD4827 Approved
0.6096 Remote Similarity NPD4828 Approved
0.6081 Remote Similarity NPD8451 Approved
0.604 Remote Similarity NPD8448 Approved
0.6027 Remote Similarity NPD8444 Approved
0.6 Remote Similarity NPD35 Approved
0.6 Remote Similarity NPD4833 Approved
0.5987 Remote Similarity NPD2101 Approved
0.5972 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5972 Remote Similarity NPD6935 Phase 3
0.5972 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5959 Remote Similarity NPD1689 Approved
0.5949 Remote Similarity NPD6077 Discontinued
0.5933 Remote Similarity NPD7746 Phase 1
0.5933 Remote Similarity NPD7747 Phase 1
0.5915 Remote Similarity NPD6429 Approved
0.5915 Remote Similarity NPD6430 Approved
0.5912 Remote Similarity NPD6122 Discontinued
0.5906 Remote Similarity NPD8342 Approved
0.5906 Remote Similarity NPD8340 Approved
0.5906 Remote Similarity NPD8341 Approved
0.5906 Remote Similarity NPD8299 Approved
0.5903 Remote Similarity NPD4830 Approved
0.5903 Remote Similarity NPD4831 Approved
0.5903 Remote Similarity NPD4832 Approved
0.589 Remote Similarity NPD2132 Phase 3
0.5887 Remote Similarity NPD1805 Phase 2
0.5887 Remote Similarity NPD1804 Phase 2
0.5878 Remote Similarity NPD8080 Discontinued
0.586 Remote Similarity NPD5767 Discontinued
0.5827 Remote Similarity NPD1385 Discontinued
0.5811 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5797 Remote Similarity NPD2258 Approved
0.5797 Remote Similarity NPD2259 Approved
0.5775 Remote Similarity NPD8087 Discontinued
0.5772 Remote Similarity NPD6436 Phase 3
0.5772 Remote Similarity NPD7623 Phase 3
0.5772 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5764 Remote Similarity NPD3731 Phase 3
0.5762 Remote Similarity NPD8273 Phase 1
0.5743 Remote Similarity NPD2645 Approved
0.5743 Remote Similarity NPD8345 Approved
0.5743 Remote Similarity NPD805 Approved
0.5743 Remote Similarity NPD8347 Approved
0.5743 Remote Similarity NPD8346 Approved
0.5743 Remote Similarity NPD806 Approved
0.5714 Remote Similarity NPD1428 Phase 2
0.5683 Remote Similarity NPD1407 Approved
0.5676 Remote Similarity NPD3159 Discontinued
0.5674 Remote Similarity NPD8140 Approved
0.5667 Remote Similarity NPD1748 Approved
0.5634 Remote Similarity NPD6686 Approved
0.5633 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5616 Remote Similarity NPD3204 Clinical (unspecified phase)
0.5608 Remote Similarity NPD6918 Phase 1
0.5608 Remote Similarity NPD1773 Discontinued

  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