Structure

Physi-Chem Properties

Molecular Weight:  461.24
Volume:  441.556
LogP:  -2.426
LogD:  -1.572
LogS:  -0.789
# Rotatable Bonds:  12
TPSA:  198.53
# H-Bond Aceptor:  12
# H-Bond Donor:  8
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.153
Synthetic Accessibility Score:  5.044
Fsp3:  0.8
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:  -6.349
MDCK Permeability:  0.00014243200712371618
Pgp-inhibitor:  0.002
Pgp-substrate:  0.992
Human Intestinal Absorption (HIA):  0.973
20% Bioavailability (F20%):  0.846
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.296
Plasma Protein Binding (PPB):  21.612957000732422%
Volume Distribution (VD):  0.335
Pgp-substrate:  78.00005340576172%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.02
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.051
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.049
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.129
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.002

ADMET: Excretion

Clearance (CL):  1.188
Half-life (T1/2):  0.701

ADMET: Toxicity

hERG Blockers:  0.1
Human Hepatotoxicity (H-HT):  0.626
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.049
Maximum Recommended Daily Dose:  0.912
Skin Sensitization:  0.206
Carcinogencity:  0.009
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.865

Download Data

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

  Natural Product: NPC471263

Natural Product ID:  NPC471263
Common Name*:   Plumbagine E Alpha-D-Xyloside
IUPAC Name:   (E,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]-7-hydroxy-6-methylhept-5-enoic acid
Synonyms:  
Standard InCHIKey:  CTAOPGCXFVDOPY-FONUMWRQSA-N
Standard InCHI:  InChI=1S/C20H35N3O9/c1-11(9-24)3-2-4-13(18(29)30)14-8-23(20(21)22-14)7-12(25)5-6-31-19-17(28)16(27)15(26)10-32-19/h3,12-17,19,24-28H,2,4-10H2,1H3,(H2,21,22)(H,29,30)/b11-3+/t12?,13-,14+,15-,16+,17-,19+/m1/s1
SMILES:  OC/C(=C/CC[C@H]([C@H]1NC(=N)N(C1)CC(CCO[C@H]1OC[C@H]([C@@H]([C@H]1O)O)O)O)C(=O)O)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407434
PubChem CID:   73356658
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[526444]
NPT461 Cell Line PANC-1 Homo sapiens IC50 > 10000.0 nM PMID[526444]

☑ 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 NPC471263 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
0.9739 High Similarity NPC471262
0.916 High Similarity NPC471255
0.904 High Similarity NPC471256
0.8435 Intermediate Similarity NPC471259
0.8174 Intermediate Similarity NPC471258
0.792 Intermediate Similarity NPC471261
0.7739 Intermediate Similarity NPC471257
0.7647 Intermediate Similarity NPC471260
0.736 Intermediate Similarity NPC147238
0.7217 Intermediate Similarity NPC304455
0.7176 Intermediate Similarity NPC314482
0.7143 Intermediate Similarity NPC3604
0.6667 Remote Similarity NPC55336
0.6641 Remote Similarity NPC315426
0.6603 Remote Similarity NPC319334
0.6603 Remote Similarity NPC321485
0.6603 Remote Similarity NPC327517
0.6603 Remote Similarity NPC317377
0.6603 Remote Similarity NPC322372
0.6567 Remote Similarity NPC6531
0.6515 Remote Similarity NPC314306
0.6493 Remote Similarity NPC30196
0.6474 Remote Similarity NPC477398
0.6449 Remote Similarity NPC20035
0.6443 Remote Similarity NPC247776
0.6443 Remote Similarity NPC475278
0.6443 Remote Similarity NPC475266
0.6443 Remote Similarity NPC309450
0.6443 Remote Similarity NPC71866
0.6443 Remote Similarity NPC304299
0.6434 Remote Similarity NPC261730
0.6434 Remote Similarity NPC475918
0.6391 Remote Similarity NPC1111
0.6391 Remote Similarity NPC261750
0.6357 Remote Similarity NPC313342
0.6357 Remote Similarity NPC64168
0.6357 Remote Similarity NPC314512
0.6357 Remote Similarity NPC314451
0.6357 Remote Similarity NPC313333
0.635 Remote Similarity NPC67917
0.635 Remote Similarity NPC314268
0.635 Remote Similarity NPC477515
0.635 Remote Similarity NPC313802
0.6316 Remote Similarity NPC477519
0.6316 Remote Similarity NPC316984
0.6316 Remote Similarity NPC30911
0.6279 Remote Similarity NPC279833
0.6279 Remote Similarity NPC173690
0.6279 Remote Similarity NPC6271
0.6279 Remote Similarity NPC80439
0.6277 Remote Similarity NPC235625
0.6269 Remote Similarity NPC60432
0.6259 Remote Similarity NPC315188
0.6241 Remote Similarity NPC121479
0.6241 Remote Similarity NPC57436
0.6214 Remote Similarity NPC94319
0.6184 Remote Similarity NPC142761
0.6176 Remote Similarity NPC259586
0.6176 Remote Similarity NPC472536
0.6176 Remote Similarity NPC103391
0.617 Remote Similarity NPC318445
0.617 Remote Similarity NPC315783
0.617 Remote Similarity NPC314629
0.617 Remote Similarity NPC316133
0.6167 Remote Similarity NPC469363
0.6159 Remote Similarity NPC106791
0.6159 Remote Similarity NPC201889
0.6154 Remote Similarity NPC314282
0.6148 Remote Similarity NPC276995
0.6148 Remote Similarity NPC76660
0.6143 Remote Similarity NPC314293
0.6131 Remote Similarity NPC470621
0.6131 Remote Similarity NPC222481
0.6127 Remote Similarity NPC36254
0.6125 Remote Similarity NPC316244
0.6124 Remote Similarity NPC188785
0.6103 Remote Similarity NPC130124
0.6103 Remote Similarity NPC193471
0.6103 Remote Similarity NPC241597
0.6093 Remote Similarity NPC315848
0.6093 Remote Similarity NPC315210
0.6087 Remote Similarity NPC209734
0.6074 Remote Similarity NPC181510
0.6074 Remote Similarity NPC168758
0.6074 Remote Similarity NPC47857
0.6054 Remote Similarity NPC314361
0.604 Remote Similarity NPC297058
0.6029 Remote Similarity NPC478024
0.6016 Remote Similarity NPC137368
0.6 Remote Similarity NPC163783
0.6 Remote Similarity NPC472199
0.6 Remote Similarity NPC472197
0.6 Remote Similarity NPC9447
0.5986 Remote Similarity NPC316401
0.5972 Remote Similarity NPC315058
0.5971 Remote Similarity NPC65045
0.5959 Remote Similarity NPC316205
0.5959 Remote Similarity NPC324722
0.5959 Remote Similarity NPC313962
0.5959 Remote Similarity NPC315387
0.5959 Remote Similarity NPC311244
0.5959 Remote Similarity NPC198644
0.5956 Remote Similarity NPC29501
0.594 Remote Similarity NPC201128
0.594 Remote Similarity NPC236644
0.5938 Remote Similarity NPC54731
0.5933 Remote Similarity NPC477400
0.5931 Remote Similarity NPC473249
0.5929 Remote Similarity NPC284656
0.5918 Remote Similarity NPC477988
0.5915 Remote Similarity NPC23963
0.5906 Remote Similarity NPC472198
0.5903 Remote Similarity NPC477985
0.5903 Remote Similarity NPC326386
0.5903 Remote Similarity NPC471087
0.5896 Remote Similarity NPC271562
0.589 Remote Similarity NPC477793
0.589 Remote Similarity NPC471086
0.589 Remote Similarity NPC329919
0.5874 Remote Similarity NPC273185
0.5865 Remote Similarity NPC74035
0.5862 Remote Similarity NPC474371
0.5862 Remote Similarity NPC309525
0.5859 Remote Similarity NPC150041
0.5855 Remote Similarity NPC287885
0.5854 Remote Similarity NPC62104
0.5854 Remote Similarity NPC1390
0.5852 Remote Similarity NPC475150
0.5846 Remote Similarity NPC315170
0.5844 Remote Similarity NPC477399
0.5844 Remote Similarity NPC477401
0.5839 Remote Similarity NPC476875
0.5833 Remote Similarity NPC111162
0.5833 Remote Similarity NPC323168
0.5833 Remote Similarity NPC293550
0.5833 Remote Similarity NPC477989
0.5833 Remote Similarity NPC477198
0.5833 Remote Similarity NPC477990
0.5833 Remote Similarity NPC325750
0.5814 Remote Similarity NPC306041
0.5806 Remote Similarity NPC304454
0.5804 Remote Similarity NPC470000
0.58 Remote Similarity NPC120420
0.5798 Remote Similarity NPC100204
0.5798 Remote Similarity NPC83248
0.5793 Remote Similarity NPC296686
0.5781 Remote Similarity NPC262312
0.5781 Remote Similarity NPC3568
0.5781 Remote Similarity NPC256570
0.5781 Remote Similarity NPC35269
0.5781 Remote Similarity NPC23454
0.5781 Remote Similarity NPC17290
0.5781 Remote Similarity NPC70323
0.5781 Remote Similarity NPC192066
0.5775 Remote Similarity NPC477237
0.5772 Remote Similarity NPC120335
0.5772 Remote Similarity NPC475472
0.5769 Remote Similarity NPC476344
0.5769 Remote Similarity NPC472736
0.5766 Remote Similarity NPC251122
0.5762 Remote Similarity NPC99864
0.5746 Remote Similarity NPC477001
0.5746 Remote Similarity NPC86095
0.5746 Remote Similarity NPC477000
0.5736 Remote Similarity NPC119225
0.5736 Remote Similarity NPC476261
0.5736 Remote Similarity NPC470382
0.5736 Remote Similarity NPC25033
0.5736 Remote Similarity NPC40663
0.5736 Remote Similarity NPC471635
0.5735 Remote Similarity NPC15413
0.5733 Remote Similarity NPC73829
0.5733 Remote Similarity NPC119794
0.5726 Remote Similarity NPC306838
0.5714 Remote Similarity NPC22883
0.5714 Remote Similarity NPC210377
0.5714 Remote Similarity NPC5719
0.5714 Remote Similarity NPC217804
0.5703 Remote Similarity NPC472196
0.5703 Remote Similarity NPC472195
0.5703 Remote Similarity NPC238090
0.5703 Remote Similarity NPC320089
0.5695 Remote Similarity NPC76999
0.5694 Remote Similarity NPC477238
0.5694 Remote Similarity NPC245534
0.5692 Remote Similarity NPC475503
0.5692 Remote Similarity NPC183449
0.5692 Remote Similarity NPC45313
0.5692 Remote Similarity NPC8098
0.5692 Remote Similarity NPC241911
0.5692 Remote Similarity NPC197294
0.5691 Remote Similarity NPC266718
0.5689 Remote Similarity NPC73655
0.5685 Remote Similarity NPC477518
0.5683 Remote Similarity NPC474497
0.5683 Remote Similarity NPC314550
0.5683 Remote Similarity NPC469466
0.5683 Remote Similarity NPC43648
0.5683 Remote Similarity NPC275100
0.5683 Remote Similarity NPC474995

  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 NPC471263 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
0.6547 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6515 Remote Similarity NPD6430 Approved
0.6515 Remote Similarity NPD6429 Approved
0.6397 Remote Similarity NPD7641 Discontinued
0.6357 Remote Similarity NPD8340 Approved
0.6357 Remote Similarity NPD8342 Approved
0.6357 Remote Similarity NPD8341 Approved
0.6357 Remote Similarity NPD8299 Approved
0.6324 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6316 Remote Similarity NPD2204 Approved
0.6259 Remote Similarity NPD8444 Approved
0.625 Remote Similarity NPD8391 Approved
0.625 Remote Similarity NPD8390 Approved
0.625 Remote Similarity NPD869 Approved
0.625 Remote Similarity NPD8392 Approved
0.6241 Remote Similarity NPD35 Approved
0.6241 Remote Similarity NPD4833 Approved
0.6214 Remote Similarity NPD4826 Approved
0.6214 Remote Similarity NPD4828 Approved
0.6214 Remote Similarity NPD4827 Approved
0.6204 Remote Similarity NPD6935 Phase 3
0.6204 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6197 Remote Similarity NPD8451 Approved
0.617 Remote Similarity NPD7830 Approved
0.617 Remote Similarity NPD7642 Approved
0.617 Remote Similarity NPD7829 Approved
0.6154 Remote Similarity NPD8448 Approved
0.6143 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6131 Remote Similarity NPD4830 Approved
0.6131 Remote Similarity NPD4831 Approved
0.6131 Remote Similarity NPD4832 Approved
0.6119 Remote Similarity NPD6421 Discontinued
0.6119 Remote Similarity NPD8087 Discontinued
0.6103 Remote Similarity NPD3731 Phase 3
0.6099 Remote Similarity NPD6436 Phase 3
0.6084 Remote Similarity NPD8273 Phase 1
0.6061 Remote Similarity NPD1385 Discontinued
0.6031 Remote Similarity NPD6122 Discontinued
0.6 Remote Similarity NPD1805 Phase 2
0.6 Remote Similarity NPD1804 Phase 2
0.5986 Remote Similarity NPD8080 Discontinued
0.596 Remote Similarity NPD5767 Discontinued
0.5957 Remote Similarity NPD8347 Approved
0.5957 Remote Similarity NPD8345 Approved
0.5957 Remote Similarity NPD8346 Approved
0.5933 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5931 Remote Similarity NPD7747 Phase 1
0.5931 Remote Similarity NPD7746 Phase 1
0.5909 Remote Similarity NPD3161 Clinical (unspecified phase)
0.5896 Remote Similarity NPD8140 Approved
0.5845 Remote Similarity NPD805 Approved
0.5845 Remote Similarity NPD806 Approved
0.5827 Remote Similarity NPD3204 Clinical (unspecified phase)
0.5821 Remote Similarity NPD1428 Phase 2
0.5816 Remote Similarity NPD6918 Phase 1
0.5789 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5778 Remote Similarity NPD8307 Discontinued
0.5764 Remote Similarity NPD7623 Phase 3
0.5764 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5762 Remote Similarity NPD8415 Approved
0.5734 Remote Similarity NPD2645 Approved
0.5692 Remote Similarity NPD6428 Approved
0.5677 Remote Similarity NPD6852 Discontinued
0.5672 Remote Similarity NPD1407 Approved
0.5671 Remote Similarity NPD8414 Discontinued
0.5669 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5655 Remote Similarity NPD1748 Approved
0.5641 Remote Similarity NPD6077 Discontinued
0.5629 Remote Similarity NPD8449 Approved
0.5625 Remote Similarity NPD1689 Approved
0.56 Remote Similarity NPD6914 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