Structure

Physi-Chem Properties

Molecular Weight:  445.24
Volume:  432.766
LogP:  -0.903
LogD:  -0.949
LogS:  -0.871
# Rotatable Bonds:  11
TPSA:  178.3
# H-Bond Aceptor:  11
# H-Bond Donor:  7
# Rings:  2
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.208
Synthetic Accessibility Score:  4.949
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:  -6.099
MDCK Permeability:  6.869626668049023e-05
Pgp-inhibitor:  0.027
Pgp-substrate:  0.997
Human Intestinal Absorption (HIA):  0.923
20% Bioavailability (F20%):  0.485
30% Bioavailability (F30%):  0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.212
Plasma Protein Binding (PPB):  31.524959564208984%
Volume Distribution (VD):  0.32
Pgp-substrate:  59.24045944213867%

ADMET: Metabolism

CYP1A2-inhibitor:  0.004
CYP1A2-substrate:  0.033
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.071
CYP2D6-inhibitor:  0.077
CYP2D6-substrate:  0.127
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.262
Half-life (T1/2):  0.593

ADMET: Toxicity

hERG Blockers:  0.13
Human Hepatotoxicity (H-HT):  0.891
Drug-inuced Liver Injury (DILI):  0.049
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.034
Maximum Recommended Daily Dose:  0.896
Skin Sensitization:  0.131
Carcinogencity:  0.031
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.896

Download Data

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

  Natural Product: NPC471262

Natural Product ID:  NPC471262
Common Name*:   Plumbagine D 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]-6-methylhept-5-enoic acid
Synonyms:  
Standard InCHIKey:  UZGVQXUOHSUMJU-RGXKXQQBSA-N
Standard InCHI:  InChI=1S/C20H35N3O8/c1-11(2)4-3-5-13(18(28)29)14-9-23(20(21)22-14)8-12(24)6-7-30-19-17(27)16(26)15(25)10-31-19/h4,12-17,19,24-27H,3,5-10H2,1-2H3,(H2,21,22)(H,28,29)/t12?,13-,14+,15-,16+,17-,19+/m1/s1
SMILES:  CC(=CCCC(C1CN(C(=N1)N)CC(CCOC2C(C(C(CO2)O)O)O)O)C(=O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2407433
PubChem CID:   71746447
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[490222]
NPT461 Cell Line PANC-1 Homo sapiens IC50 > 10000.0 nM PMID[490222]

☑ 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 NPC471262 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 NPC471263
0.9397 High Similarity NPC471255
0.8952 High Similarity NPC471256
0.8393 Intermediate Similarity NPC471258
0.8174 Intermediate Similarity NPC471259
0.7845 Intermediate Similarity NPC471260
0.7823 Intermediate Similarity NPC471261
0.7478 Intermediate Similarity NPC471257
0.7411 Intermediate Similarity NPC304455
0.7328 Intermediate Similarity NPC3604
0.7258 Intermediate Similarity NPC147238
0.6947 Remote Similarity NPC314482
0.6601 Remote Similarity NPC477398
0.6587 Remote Similarity NPC475918
0.6538 Remote Similarity NPC261750
0.6538 Remote Similarity NPC1111
0.6516 Remote Similarity NPC327517
0.6516 Remote Similarity NPC321485
0.6516 Remote Similarity NPC322372
0.6516 Remote Similarity NPC319334
0.6516 Remote Similarity NPC317377
0.6429 Remote Similarity NPC55336
0.6412 Remote Similarity NPC60432
0.6406 Remote Similarity NPC315426
0.6385 Remote Similarity NPC121479
0.6385 Remote Similarity NPC57436
0.635 Remote Similarity NPC94319
0.6343 Remote Similarity NPC6531
0.6338 Remote Similarity NPC261730
0.6325 Remote Similarity NPC469363
0.6316 Remote Similarity NPC259586
0.6304 Remote Similarity NPC314629
0.6288 Remote Similarity NPC314306
0.6269 Remote Similarity NPC222481
0.6269 Remote Similarity NPC470621
0.6269 Remote Similarity NPC30196
0.625 Remote Similarity NPC314268
0.625 Remote Similarity NPC64168
0.625 Remote Similarity NPC477515
0.625 Remote Similarity NPC313802
0.625 Remote Similarity NPC67917
0.6242 Remote Similarity NPC71866
0.6242 Remote Similarity NPC309450
0.6242 Remote Similarity NPC475266
0.6242 Remote Similarity NPC304299
0.6242 Remote Similarity NPC247776
0.6242 Remote Similarity NPC475278
0.6241 Remote Similarity NPC241597
0.6232 Remote Similarity NPC20035
0.6225 Remote Similarity NPC477519
0.6212 Remote Similarity NPC30911
0.6212 Remote Similarity NPC316984
0.6176 Remote Similarity NPC235625
0.6172 Remote Similarity NPC6271
0.6172 Remote Similarity NPC173690
0.6172 Remote Similarity NPC279833
0.6172 Remote Similarity NPC80439
0.6143 Remote Similarity NPC314451
0.6143 Remote Similarity NPC313333
0.6143 Remote Similarity NPC313342
0.6143 Remote Similarity NPC314512
0.6127 Remote Similarity NPC163783
0.6093 Remote Similarity NPC142761
0.6084 Remote Similarity NPC316205
0.6084 Remote Similarity NPC315387
0.6074 Remote Similarity NPC103391
0.6074 Remote Similarity NPC472536
0.6071 Remote Similarity NPC316133
0.6071 Remote Similarity NPC318445
0.6071 Remote Similarity NPC315783
0.6058 Remote Similarity NPC201889
0.6058 Remote Similarity NPC106791
0.6056 Remote Similarity NPC314282
0.6054 Remote Similarity NPC477400
0.6045 Remote Similarity NPC276995
0.6045 Remote Similarity NPC76660
0.6043 Remote Similarity NPC315188
0.6038 Remote Similarity NPC316244
0.6 Remote Similarity NPC193471
0.6 Remote Similarity NPC130124
0.5986 Remote Similarity NPC309525
0.5985 Remote Similarity NPC209734
0.5973 Remote Similarity NPC287885
0.597 Remote Similarity NPC476875
0.5969 Remote Similarity NPC477198
0.5963 Remote Similarity NPC62104
0.5963 Remote Similarity NPC1390
0.596 Remote Similarity NPC477401
0.596 Remote Similarity NPC477399
0.595 Remote Similarity NPC304454
0.5948 Remote Similarity NPC100204
0.5948 Remote Similarity NPC83248
0.5946 Remote Similarity NPC297058
0.5929 Remote Similarity NPC314293
0.5926 Remote Similarity NPC478024
0.5915 Remote Similarity NPC36254
0.5915 Remote Similarity NPC296686
0.5906 Remote Similarity NPC472736
0.5899 Remote Similarity NPC477237
0.5894 Remote Similarity NPC315848
0.5894 Remote Similarity NPC315210
0.5891 Remote Similarity NPC188785
0.589 Remote Similarity NPC475472
0.589 Remote Similarity NPC316401
0.5887 Remote Similarity NPC9447
0.5873 Remote Similarity NPC470382
0.5873 Remote Similarity NPC119225
0.5873 Remote Similarity NPC476261
0.5873 Remote Similarity NPC471635
0.5873 Remote Similarity NPC40663
0.5873 Remote Similarity NPC25033
0.587 Remote Similarity NPC65045
0.5868 Remote Similarity NPC306838
0.5865 Remote Similarity NPC15413
0.5862 Remote Similarity NPC198644
0.5862 Remote Similarity NPC311244
0.5862 Remote Similarity NPC324722
0.5852 Remote Similarity NPC168758
0.5852 Remote Similarity NPC181510
0.5852 Remote Similarity NPC47857
0.585 Remote Similarity NPC314361
0.585 Remote Similarity NPC119794
0.585 Remote Similarity NPC73829
0.5833 Remote Similarity NPC236644
0.5827 Remote Similarity NPC284656
0.5827 Remote Similarity NPC54731
0.5818 Remote Similarity NPC217804
0.5818 Remote Similarity NPC22883
0.5818 Remote Similarity NPC210377
0.5818 Remote Similarity NPC5719
0.5816 Remote Similarity NPC23963
0.5816 Remote Similarity NPC477238
0.5811 Remote Similarity NPC76999
0.5804 Remote Similarity NPC477518
0.5804 Remote Similarity NPC471087
0.5804 Remote Similarity NPC326386
0.5804 Remote Similarity NPC477985
0.5798 Remote Similarity NPC165119
0.5793 Remote Similarity NPC73655
0.5789 Remote Similarity NPC271562
0.5789 Remote Similarity NPC210729
0.5789 Remote Similarity NPC172365
0.5789 Remote Similarity NPC82931
0.5785 Remote Similarity NPC477746
0.5785 Remote Similarity NPC477747
0.5782 Remote Similarity NPC15249
0.5782 Remote Similarity NPC25455
0.5772 Remote Similarity NPC75318
0.5772 Remote Similarity NPC280941
0.5772 Remote Similarity NPC137368
0.5772 Remote Similarity NPC235772
0.5764 Remote Similarity NPC315058
0.5764 Remote Similarity NPC474371
0.576 Remote Similarity NPC472197
0.576 Remote Similarity NPC475603
0.576 Remote Similarity NPC472199
0.576 Remote Similarity NPC208537
0.576 Remote Similarity NPC61894
0.576 Remote Similarity NPC270005
0.5758 Remote Similarity NPC62845
0.5758 Remote Similarity NPC166242
0.5758 Remote Similarity NPC189854
0.5758 Remote Similarity NPC92874
0.5758 Remote Similarity NPC322449
0.5753 Remote Similarity NPC313962
0.5749 Remote Similarity NPC63040
0.5746 Remote Similarity NPC171734
0.5745 Remote Similarity NPC139867
0.5743 Remote Similarity NPC122819
0.5735 Remote Similarity NPC29501
0.5734 Remote Similarity NPC477990
0.5734 Remote Similarity NPC325750
0.5734 Remote Similarity NPC323168
0.5734 Remote Similarity NPC477989
0.5734 Remote Similarity NPC111162
0.5734 Remote Similarity NPC293550
0.5733 Remote Similarity NPC145899
0.5726 Remote Similarity NPC159369
0.5726 Remote Similarity NPC39290
0.5726 Remote Similarity NPC98750
0.5725 Remote Similarity NPC227622
0.5725 Remote Similarity NPC471097
0.5725 Remote Similarity NPC475149
0.5724 Remote Similarity NPC473249
0.5714 Remote Similarity NPC475584
0.5714 Remote Similarity NPC201128
0.5714 Remote Similarity NPC325900
0.5714 Remote Similarity NPC475152
0.5714 Remote Similarity NPC475394
0.5714 Remote Similarity NPC477988
0.5714 Remote Similarity NPC10897
0.5705 Remote Similarity NPC120420
0.5705 Remote Similarity NPC147753
0.5705 Remote Similarity NPC150057
0.5704 Remote Similarity NPC470000
0.5703 Remote Similarity NPC306041
0.5689 Remote Similarity NPC15068
0.5685 Remote Similarity NPC471086
0.5685 Remote Similarity NPC477793
0.5685 Remote Similarity NPC329919

  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 NPC471262 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
0.6541 Remote Similarity NPD7641 Discontinued
0.6466 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6385 Remote Similarity NPD4833 Approved
0.6385 Remote Similarity NPD35 Approved
0.635 Remote Similarity NPD4827 Approved
0.635 Remote Similarity NPD4828 Approved
0.635 Remote Similarity NPD4826 Approved
0.6343 Remote Similarity NPD6935 Phase 3
0.6343 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6331 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6288 Remote Similarity NPD6429 Approved
0.6288 Remote Similarity NPD6430 Approved
0.6277 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6269 Remote Similarity NPD4831 Approved
0.6269 Remote Similarity NPD4830 Approved
0.6269 Remote Similarity NPD4832 Approved
0.626 Remote Similarity NPD8087 Discontinued
0.6241 Remote Similarity NPD3731 Phase 3
0.6232 Remote Similarity NPD6436 Phase 3
0.6212 Remote Similarity NPD2204 Approved
0.6172 Remote Similarity NPD6122 Discontinued
0.6159 Remote Similarity NPD8444 Approved
0.6154 Remote Similarity NPD8390 Approved
0.6154 Remote Similarity NPD8391 Approved
0.6154 Remote Similarity NPD8392 Approved
0.6143 Remote Similarity NPD8341 Approved
0.6143 Remote Similarity NPD8340 Approved
0.6143 Remote Similarity NPD8299 Approved
0.6143 Remote Similarity NPD8342 Approved
0.6136 Remote Similarity NPD1805 Phase 2
0.6136 Remote Similarity NPD1804 Phase 2
0.6115 Remote Similarity NPD8080 Discontinued
0.6099 Remote Similarity NPD8451 Approved
0.6087 Remote Similarity NPD8347 Approved
0.6087 Remote Similarity NPD8345 Approved
0.6087 Remote Similarity NPD8346 Approved
0.6071 Remote Similarity NPD7829 Approved
0.6071 Remote Similarity NPD7830 Approved
0.6071 Remote Similarity NPD7642 Approved
0.6056 Remote Similarity NPD8448 Approved
0.6047 Remote Similarity NPD3161 Clinical (unspecified phase)
0.6031 Remote Similarity NPD8140 Approved
0.6029 Remote Similarity NPD869 Approved
0.5956 Remote Similarity NPD3204 Clinical (unspecified phase)
0.5954 Remote Similarity NPD1428 Phase 2
0.5954 Remote Similarity NPD1385 Discontinued
0.5942 Remote Similarity NPD6918 Phase 1
0.5923 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5909 Remote Similarity NPD8307 Discontinued
0.5896 Remote Similarity NPD6421 Discontinued
0.5874 Remote Similarity NPD8273 Phase 1
0.5827 Remote Similarity NPD6428 Approved
0.5789 Remote Similarity NPD6852 Discontinued
0.5762 Remote Similarity NPD5767 Discontinued
0.5752 Remote Similarity NPD6077 Discontinued
0.5745 Remote Similarity NPD1689 Approved
0.5743 Remote Similarity NPD8449 Approved
0.5733 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5726 Remote Similarity NPD3716 Discontinued
0.5725 Remote Similarity NPD8139 Approved
0.5725 Remote Similarity NPD8086 Approved
0.5725 Remote Similarity NPD8085 Approved
0.5725 Remote Similarity NPD8083 Approved
0.5725 Remote Similarity NPD8138 Approved
0.5725 Remote Similarity NPD8082 Approved
0.5725 Remote Similarity NPD8084 Approved
0.5724 Remote Similarity NPD7746 Phase 1
0.5724 Remote Similarity NPD7747 Phase 1
0.5705 Remote Similarity NPD8450 Suspended
0.5704 Remote Similarity NPD8305 Approved
0.5704 Remote Similarity NPD8306 Approved
0.5695 Remote Similarity NPD4153 Approved
0.5685 Remote Similarity NPD8337 Approved
0.5685 Remote Similarity NPD8336 Approved
0.5682 Remote Similarity NPD4743 Phase 2
0.5682 Remote Similarity NPD8276 Approved
0.5682 Remote Similarity NPD8275 Approved
0.5676 Remote Similarity NPD2101 Approved
0.5667 Remote Similarity NPD8415 Approved
0.5639 Remote Similarity NPD8081 Approved
0.5634 Remote Similarity NPD805 Approved
0.5634 Remote Similarity NPD806 Approved
0.5625 Remote Similarity NPD2621 Clinical (unspecified phase)
0.5625 Remote Similarity NPD7844 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