Structure

Physi-Chem Properties

Molecular Weight:  630.34
Volume:  591.184
LogP:  -3.932
LogD:  -1.623
LogS:  -1.064
# Rotatable Bonds:  18
TPSA:  334.7
# H-Bond Aceptor:  19
# H-Bond Donor:  17
# Rings:  3
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.081
Synthetic Accessibility Score:  5.624
Fsp3:  0.76
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.077
MDCK Permeability:  8.170741784851998e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.96
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.843
Plasma Protein Binding (PPB):  9.007719039916992%
Volume Distribution (VD):  0.442
Pgp-substrate:  82.14136505126953%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.012
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.028
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.001
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.016
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.06

ADMET: Excretion

Clearance (CL):  1.419
Half-life (T1/2):  0.708

ADMET: Toxicity

hERG Blockers:  0.211
Human Hepatotoxicity (H-HT):  0.977
Drug-inuced Liver Injury (DILI):  0.027
AMES Toxicity:  0.182
Rat Oral Acute Toxicity:  0.072
Maximum Recommended Daily Dose:  0.992
Skin Sensitization:  0.155
Carcinogencity:  0.377
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.926

Download Data

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

  Natural Product: NPC314398

Natural Product ID:  NPC314398
Common Name*:   Streptothricin E
IUPAC Name:   [(2R,3R,4S,5R,6R)-6-[[(3aS,7R,7aS)-7-hydroxy-4-oxo-1,3a,5,6,7,7a-hexahydroimidazo[4,5-c]pyridin-2-yl]amino]-5-[[(3S)-3-amino-6-[[(3S)-3,6-diaminohexanoyl]amino]hexanoyl]amino]-4-hydroxy-2-(hydroxymethyl)oxan-3-yl] carbamate
Synonyms:   streptothricin E
Standard InCHIKey:  SCHKAKNJXBPJHD-SNQQVPMJSA-N
Standard InCHI:  InChI=1S/C25H46N10O9/c26-5-1-3-11(27)7-15(38)30-6-2-4-12(28)8-16(39)32-19-20(40)21(44-24(29)42)14(10-36)43-23(19)35-25-33-17-13(37)9-31-22(41)18(17)34-25/h11-14,17-21,23,36-37,40H,1-10,26-28H2,(H2,29,42)(H,30,38)(H,31,41)(H,32,39)(H2,33,34,35)/t11-,12-,13+,14+,17+,18-,19+,20-,21-,23+/m0/s1
SMILES:  C1C(C2C(C(=O)N1)N=C(N2)NC3C(C(C(C(O3)CO)OC(=O)N)O)NC(=O)CC(CCCNC(=O)CC(CCCN)N)N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1801945
PubChem CID:   160718
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:0002203] Glycosylamines

*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
NPO31206 Streptomyces sp. i08a 1776 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21510638]
NPO31206 Streptomyces sp. i08a 1776 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[22939698]

☑ 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
NPT81 Cell Line A549 Homo sapiens IC50 > 10000.0 nM PMID[538074]
NPT65 Cell Line HepG2 Homo sapiens IC50 > 10000.0 nM PMID[538074]
NPT165 Cell Line HeLa Homo sapiens IC50 > 10000.0 nM PMID[538074]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 4.0 ug.mL-1 PMID[538074]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 64.0 ug.mL-1 PMID[538074]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 1.0 ug.mL-1 PMID[538074]
NPT1107 Organism Mycobacterium smegmatis str. MC2 155 Mycobacterium smegmatis str. MC2 155 MIC = 4.0 ug.mL-1 PMID[538074]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 16.0 ug.mL-1 PMID[538074]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 64.0 ug.mL-1 PMID[538074]
NPT3495 Organism Morganella morganii Morganella morganii MIC = 4.0 ug.mL-1 PMID[538074]
NPT19 Organism Escherichia coli Escherichia coli MIC = 16.0 ug.mL-1 PMID[538074]
NPT20 Organism Candida albicans Candida albicans MIC = 1.0 ug.mL-1 PMID[538074]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 4.0 ug.mL-1 PMID[538075]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 64.0 ug.mL-1 PMID[538075]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 1.0 ug.mL-1 PMID[538075]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC = 1.0 ug.mL-1 PMID[538075]
NPT1107 Organism Mycobacterium smegmatis str. MC2 155 Mycobacterium smegmatis str. MC2 155 MIC = 4.0 ug.mL-1 PMID[538075]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 0.5 ug.mL-1 PMID[538075]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis MIC = 0.25 ug.mL-1 PMID[538075]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 64.0 ug.mL-1 PMID[538075]
NPT3495 Organism Morganella morganii Morganella morganii MIC = 4.0 ug.mL-1 PMID[538075]
NPT19 Organism Escherichia coli Escherichia coli MIC = 16.0 ug.mL-1 PMID[538075]
NPT20 Organism Candida albicans Candida albicans MIC = 1.0 ug.mL-1 PMID[538075]
NPT88 Organism Mycobacterium tuberculosis Mycobacterium tuberculosis Ratio = 8.0 n.a. PMID[538075]
NPT2 Others Unspecified Ratio = 0.1 n.a. PMID[538076]
NPT2 Others Unspecified EC50 = 400.0 nM PMID[538076]

☑ 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 NPC314398 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
1.0 High Similarity NPC314413
1.0 High Similarity NPC239705
0.9896 High Similarity NPC92874
0.9896 High Similarity NPC62845
0.9896 High Similarity NPC322449
0.9896 High Similarity NPC166242
0.9896 High Similarity NPC189854
0.9794 High Similarity NPC10897
0.9794 High Similarity NPC325900
0.8519 High Similarity NPC259586
0.844 Intermediate Similarity NPC222481
0.844 Intermediate Similarity NPC470621
0.6897 Remote Similarity NPC121479
0.6897 Remote Similarity NPC57436
0.6891 Remote Similarity NPC313813
0.6759 Remote Similarity NPC216278
0.6486 Remote Similarity NPC330590
0.6364 Remote Similarity NPC315806
0.6356 Remote Similarity NPC59589
0.6355 Remote Similarity NPC306838
0.6299 Remote Similarity NPC94319
0.6214 Remote Similarity NPC316807
0.6154 Remote Similarity NPC100204
0.6154 Remote Similarity NPC70574
0.6154 Remote Similarity NPC318258
0.6154 Remote Similarity NPC83248
0.6147 Remote Similarity NPC214376
0.6132 Remote Similarity NPC165119
0.6121 Remote Similarity NPC315036
0.6117 Remote Similarity NPC314772
0.6117 Remote Similarity NPC314968
0.6058 Remote Similarity NPC98750
0.6055 Remote Similarity NPC313552
0.6038 Remote Similarity NPC271772
0.6038 Remote Similarity NPC36927
0.6036 Remote Similarity NPC176381
0.6036 Remote Similarity NPC195969
0.6019 Remote Similarity NPC329077
0.6 Remote Similarity NPC43850
0.6 Remote Similarity NPC477060
0.6 Remote Similarity NPC325750
0.6 Remote Similarity NPC314408
0.6 Remote Similarity NPC314007
0.6 Remote Similarity NPC123746
0.5983 Remote Similarity NPC56298
0.5983 Remote Similarity NPC471628
0.5954 Remote Similarity NPC477518
0.5929 Remote Similarity NPC328646
0.5909 Remote Similarity NPC62927
0.5909 Remote Similarity NPC190334
0.59 Remote Similarity NPC327753
0.59 Remote Similarity NPC327486
0.59 Remote Similarity NPC223174
0.5888 Remote Similarity NPC242077
0.5877 Remote Similarity NPC315334
0.5856 Remote Similarity NPC328806
0.5839 Remote Similarity NPC318142
0.5833 Remote Similarity NPC263058
0.5825 Remote Similarity NPC474467
0.5818 Remote Similarity NPC469363
0.5804 Remote Similarity NPC275715
0.5776 Remote Similarity NPC90240
0.5763 Remote Similarity NPC328914
0.5758 Remote Similarity NPC322801
0.5758 Remote Similarity NPC129100
0.5758 Remote Similarity NPC291650
0.5741 Remote Similarity NPC315969
0.5726 Remote Similarity NPC328779
0.5714 Remote Similarity NPC68327
0.57 Remote Similarity NPC316445
0.569 Remote Similarity NPC280946
0.569 Remote Similarity NPC226769
0.569 Remote Similarity NPC6166
0.5682 Remote Similarity NPC471262
0.5682 Remote Similarity NPC139857
0.5672 Remote Similarity NPC315058
0.5664 Remote Similarity NPC470284
0.5662 Remote Similarity NPC313962
0.566 Remote Similarity NPC325902
0.5657 Remote Similarity NPC315980
0.5652 Remote Similarity NPC270005
0.5652 Remote Similarity NPC208537
0.5648 Remote Similarity NPC471420
0.5645 Remote Similarity NPC149843
0.5645 Remote Similarity NPC155087
0.5641 Remote Similarity NPC120887
0.5636 Remote Similarity NPC229249
0.5631 Remote Similarity NPC474468
0.5621 Remote Similarity NPC317377
0.5621 Remote Similarity NPC319334
0.5621 Remote Similarity NPC321485
0.5621 Remote Similarity NPC327517
0.5621 Remote Similarity NPC322372
0.5606 Remote Similarity NPC245534

  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 NPC314398 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
0.7009 Intermediate Similarity NPD6424 Approved
0.697 Remote Similarity NPD9429 Discontinued
0.6957 Remote Similarity NPD284 Phase 1
0.6897 Remote Similarity NPD4833 Approved
0.6897 Remote Similarity NPD35 Approved
0.6814 Remote Similarity NPD8045 Clinical (unspecified phase)
0.6759 Remote Similarity NPD6426 Approved
0.6759 Remote Similarity NPD6423 Approved
0.6759 Remote Similarity NPD6427 Approved
0.6759 Remote Similarity NPD6425 Approved
0.6729 Remote Similarity NPD6431 Approved
0.6729 Remote Similarity NPD6432 Approved
0.6729 Remote Similarity NPD6434 Clinical (unspecified phase)
0.6729 Remote Similarity NPD6433 Approved
0.6667 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6552 Remote Similarity NPD5376 Approved
0.6486 Remote Similarity NPD5377 Approved
0.6486 Remote Similarity NPD5381 Approved
0.6486 Remote Similarity NPD5378 Approved
0.64 Remote Similarity NPD9407 Approved
0.6364 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6299 Remote Similarity NPD4826 Approved
0.6299 Remote Similarity NPD4828 Approved
0.6299 Remote Similarity NPD4827 Approved
0.6283 Remote Similarity NPD6428 Approved
0.626 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6182 Remote Similarity NPD3716 Discontinued
0.6168 Remote Similarity NPD9654 Phase 2
0.6162 Remote Similarity NPD5386 Phase 2
0.6147 Remote Similarity NPD2698 Approved
0.6117 Remote Similarity NPD9435 Approved
0.6117 Remote Similarity NPD9434 Approved
0.61 Remote Similarity NPD9405 Approved
0.6087 Remote Similarity NPD4282 Approved
0.608 Remote Similarity NPD869 Approved
0.6036 Remote Similarity NPD5796 Clinical (unspecified phase)
0.6036 Remote Similarity NPD5797 Approved
0.6036 Remote Similarity NPD5798 Approved
0.6036 Remote Similarity NPD5794 Approved
0.6036 Remote Similarity NPD5795 Approved
0.6031 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6017 Remote Similarity NPD1061 Clinical (unspecified phase)
0.6 Remote Similarity NPD3201 Approved
0.6 Remote Similarity NPD3207 Approved
0.6 Remote Similarity NPD3203 Approved
0.6 Remote Similarity NPD3209 Approved
0.6 Remote Similarity NPD3202 Approved
0.6 Remote Similarity NPD3208 Approved
0.5983 Remote Similarity NPD4838 Approved
0.5983 Remote Similarity NPD4836 Approved
0.5983 Remote Similarity NPD4835 Approved
0.5983 Remote Similarity NPD4837 Approved
0.5982 Remote Similarity NPD9585 Discontinued
0.5982 Remote Similarity NPD6943 Clinical (unspecified phase)
0.596 Remote Similarity NPD3213 Discontinued
0.5935 Remote Similarity NPD1805 Phase 2
0.5935 Remote Similarity NPD1804 Phase 2
0.5923 Remote Similarity NPD6436 Phase 3
0.5917 Remote Similarity NPD6946 Approved
0.5917 Remote Similarity NPD2700 Approved
0.5913 Remote Similarity NPD7844 Discontinued
0.5909 Remote Similarity NPD9603 Phase 3
0.5909 Remote Similarity NPD9604 Approved
0.5909 Remote Similarity NPD3200 Clinical (unspecified phase)
0.5909 Remote Similarity NPD9602 Phase 3
0.59 Remote Similarity NPD9445 Approved
0.59 Remote Similarity NPD2704 Phase 3
0.59 Remote Similarity NPD2702 Phase 1
0.5897 Remote Similarity NPD223 Clinical (unspecified phase)
0.5888 Remote Similarity NPD9644 Approved
0.5888 Remote Similarity NPD9645 Approved
0.5888 Remote Similarity NPD9646 Approved
0.5868 Remote Similarity NPD1428 Phase 2
0.5841 Remote Similarity NPD285 Discontinued
0.5816 Remote Similarity NPD2703 Discontinued
0.5763 Remote Similarity NPD1454 Phase 3
0.5763 Remote Similarity NPD1455 Phase 3
0.5758 Remote Similarity NPD9031 Approved
0.5758 Remote Similarity NPD373 Approved
0.5758 Remote Similarity NPD9033 Approved
0.5758 Remote Similarity NPD9032 Approved
0.5758 Remote Similarity NPD9030 Approved
0.5758 Remote Similarity NPD374 Approved
0.5714 Remote Similarity NPD591 Approved
0.5714 Remote Similarity NPD577 Phase 3
0.5702 Remote Similarity NPD4743 Phase 2
0.5688 Remote Similarity NPD4829 Discontinued
0.5636 Remote Similarity NPD9601 Approved
0.5625 Remote Similarity NPD241 Discontinued
0.5625 Remote Similarity NPD3138 Phase 3
0.5625 Remote Similarity NPD1760 Approved
0.561 Remote Similarity NPD1385 Discontinued
0.56 Remote Similarity NPD6941 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