Structure

Physi-Chem Properties

Molecular Weight:  379.16
Volume:  340.417
LogP:  -2.504
LogD:  -1.803
LogS:  -0.461
# Rotatable Bonds:  4
TPSA:  221.31
# H-Bond Aceptor:  12
# H-Bond Donor:  10
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.172
Synthetic Accessibility Score:  4.965
Fsp3:  0.857
Lipinski Rule-of-5:  Rejected
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:  -6.488
MDCK Permeability:  0.00020696708816103637
Pgp-inhibitor:  0.001
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.985
20% Bioavailability (F20%):  0.168
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.295
Plasma Protein Binding (PPB):  14.046623229980469%
Volume Distribution (VD):  0.286
Pgp-substrate:  85.40491485595703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.019
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.047
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.054
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.117
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.008

ADMET: Excretion

Clearance (CL):  1.405
Half-life (T1/2):  0.664

ADMET: Toxicity

hERG Blockers:  0.161
Human Hepatotoxicity (H-HT):  0.147
Drug-inuced Liver Injury (DILI):  0.06
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.005
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.109
Carcinogencity:  0.051
Eye Corrosion:  0.003
Eye Irritation:  0.056
Respiratory Toxicity:  0.922

Download Data

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

  Natural Product: NPC328646

Natural Product ID:  NPC328646
Common Name*:   Kasugamycin
IUPAC Name:   n.a.
Synonyms:   Kasugamycin
Standard InCHIKey:  PVTHJAPFENJVNC-MHRBZPPQSA-N
Standard InCHI:  InChI=1S/C14H25N3O9/c1-3-5(17-12(16)13(23)24)2-4(15)14(25-3)26-11-9(21)7(19)6(18)8(20)10(11)22/h3-11,14,18-22H,2,15H2,1H3,(H2,16,17)(H,23,24)/t3-,4+,5+,6-,7+,8+,9-,10+,11+,14-/m1/s1
SMILES:  N[C@H]1C[C@H](N=C(C(=O)O)N)[C@H](O[C@@H]1O[C@@H]1[C@@H](O)[C@@H](O)[C@@H]([C@@H]([C@H]1O)O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1631109
PubChem CID:   NA
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0003335] Glyco-alpha-amino acids

*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
NPO14945 Streptomyces kasugaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[16998486]

☑ 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
NPT19 Organism Escherichia coli Escherichia coli MIC = 200.0 ug.mL-1 PMID[457262]
NPT2709 Organism Bacillus subtilis subsp. subtilis str. 168 Bacillus subtilis subsp. subtilis str. 168 MIC = 1500.0 ug.mL-1 PMID[457262]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 500.0 ug.mL-1 PMID[457262]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 1500.0 ug.mL-1 PMID[457262]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 5000.0 ug.mL-1 PMID[457262]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 4000.0 ug.mL-1 PMID[457262]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 15000.0 ug.mL-1 PMID[457262]

☑ 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 NPC328646 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
0.7475 Intermediate Similarity NPC330590
0.7391 Intermediate Similarity NPC315969
0.7312 Intermediate Similarity NPC263058
0.7253 Intermediate Similarity NPC316807
0.7188 Intermediate Similarity NPC313552
0.7113 Intermediate Similarity NPC43850
0.7113 Intermediate Similarity NPC214376
0.7113 Intermediate Similarity NPC314408
0.7113 Intermediate Similarity NPC123746
0.7113 Intermediate Similarity NPC477060
0.7113 Intermediate Similarity NPC314007
0.7 Intermediate Similarity NPC208537
0.7 Intermediate Similarity NPC270005
0.6989 Remote Similarity NPC318258
0.6989 Remote Similarity NPC70574
0.697 Remote Similarity NPC195969
0.697 Remote Similarity NPC176381
0.6882 Remote Similarity NPC98750
0.6842 Remote Similarity NPC271772
0.6842 Remote Similarity NPC36927
0.6822 Remote Similarity NPC221148
0.6804 Remote Similarity NPC192025
0.6804 Remote Similarity NPC125253
0.6804 Remote Similarity NPC253975
0.6774 Remote Similarity NPC314968
0.6774 Remote Similarity NPC314772
0.6765 Remote Similarity NPC315334
0.6757 Remote Similarity NPC57436
0.6757 Remote Similarity NPC121479
0.6742 Remote Similarity NPC327486
0.6742 Remote Similarity NPC223174
0.6742 Remote Similarity NPC327753
0.6735 Remote Similarity NPC83839
0.6699 Remote Similarity NPC470283
0.6698 Remote Similarity NPC315036
0.6632 Remote Similarity NPC100204
0.6632 Remote Similarity NPC83248
0.6591 Remote Similarity NPC129100
0.6591 Remote Similarity NPC291650
0.6591 Remote Similarity NPC322801
0.6542 Remote Similarity NPC56298
0.6542 Remote Similarity NPC471628
0.6526 Remote Similarity NPC150557
0.6465 Remote Similarity NPC476523
0.6436 Remote Similarity NPC470282
0.6429 Remote Similarity NPC165119
0.6417 Remote Similarity NPC94319
0.6392 Remote Similarity NPC471420
0.6373 Remote Similarity NPC470284
0.6337 Remote Similarity NPC306838
0.633 Remote Similarity NPC42320
0.633 Remote Similarity NPC188453
0.625 Remote Similarity NPC475918
0.6214 Remote Similarity NPC292345
0.6186 Remote Similarity NPC313813
0.6102 Remote Similarity NPC259586
0.6053 Remote Similarity NPC59589
0.605 Remote Similarity NPC222481
0.605 Remote Similarity NPC470621
0.6038 Remote Similarity NPC475603
0.6038 Remote Similarity NPC61894
0.6018 Remote Similarity NPC189854
0.6018 Remote Similarity NPC166242
0.6018 Remote Similarity NPC322449
0.6018 Remote Similarity NPC92874
0.6018 Remote Similarity NPC62845
0.5965 Remote Similarity NPC10897
0.5965 Remote Similarity NPC325900
0.5929 Remote Similarity NPC314398
0.5929 Remote Similarity NPC239705
0.5929 Remote Similarity NPC314413
0.5882 Remote Similarity NPC241597
0.5833 Remote Similarity NPC476248
0.5795 Remote Similarity NPC320032
0.5769 Remote Similarity NPC469363
0.5761 Remote Similarity NPC76881
0.5761 Remote Similarity NPC12040
0.5761 Remote Similarity NPC190418
0.5761 Remote Similarity NPC471761
0.5761 Remote Similarity NPC471760
0.5743 Remote Similarity NPC314466
0.5741 Remote Similarity NPC473581
0.5741 Remote Similarity NPC111567
0.5741 Remote Similarity NPC15851
0.5741 Remote Similarity NPC263545
0.5741 Remote Similarity NPC309898
0.5741 Remote Similarity NPC186840
0.5741 Remote Similarity NPC282705
0.5741 Remote Similarity NPC473950
0.5741 Remote Similarity NPC182632
0.5741 Remote Similarity NPC475125
0.5741 Remote Similarity NPC473604
0.5729 Remote Similarity NPC55274
0.5698 Remote Similarity NPC303727
0.5648 Remote Similarity NPC209047
0.5648 Remote Similarity NPC242503
0.5648 Remote Similarity NPC139782
0.5648 Remote Similarity NPC74672
0.5648 Remote Similarity NPC43074
0.5641 Remote Similarity NPC317534
0.5636 Remote Similarity NPC158445
0.5636 Remote Similarity NPC23454
0.5636 Remote Similarity NPC35269
0.5636 Remote Similarity NPC256570
0.5636 Remote Similarity NPC3568
0.5636 Remote Similarity NPC54961
0.5636 Remote Similarity NPC282088
0.5636 Remote Similarity NPC70323
0.5636 Remote Similarity NPC192066
0.5636 Remote Similarity NPC17290
0.5636 Remote Similarity NPC262312
0.5636 Remote Similarity NPC157353
0.5636 Remote Similarity NPC156782
0.56 Remote Similarity NPC37681

  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 NPC328646 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
0.7755 Intermediate Similarity NPD6428 Approved
0.7475 Intermediate Similarity NPD5378 Approved
0.7475 Intermediate Similarity NPD5381 Approved
0.7475 Intermediate Similarity NPD5377 Approved
0.7308 Intermediate Similarity NPD8045 Clinical (unspecified phase)
0.7188 Intermediate Similarity NPD3200 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD3716 Discontinued
0.7113 Intermediate Similarity NPD3201 Approved
0.7113 Intermediate Similarity NPD3208 Approved
0.7113 Intermediate Similarity NPD3202 Approved
0.7113 Intermediate Similarity NPD3209 Approved
0.7113 Intermediate Similarity NPD2698 Approved
0.7113 Intermediate Similarity NPD3207 Approved
0.7113 Intermediate Similarity NPD3203 Approved
0.7009 Intermediate Similarity NPD5376 Approved
0.697 Remote Similarity NPD5797 Approved
0.697 Remote Similarity NPD5794 Approved
0.697 Remote Similarity NPD5795 Approved
0.697 Remote Similarity NPD5796 Clinical (unspecified phase)
0.697 Remote Similarity NPD5798 Approved
0.6822 Remote Similarity NPD1450 Approved
0.6822 Remote Similarity NPD1449 Approved
0.6818 Remote Similarity NPD6941 Approved
0.6774 Remote Similarity NPD9434 Approved
0.6774 Remote Similarity NPD9435 Approved
0.6768 Remote Similarity NPD4759 Clinical (unspecified phase)
0.6765 Remote Similarity NPD1446 Phase 3
0.6765 Remote Similarity NPD1447 Phase 3
0.6759 Remote Similarity NPD2700 Approved
0.6757 Remote Similarity NPD35 Approved
0.6757 Remote Similarity NPD4833 Approved
0.6742 Remote Similarity NPD9445 Approved
0.6667 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4282 Approved
0.6591 Remote Similarity NPD9033 Approved
0.6591 Remote Similarity NPD9032 Approved
0.6591 Remote Similarity NPD9030 Approved
0.6591 Remote Similarity NPD9031 Approved
0.6542 Remote Similarity NPD4835 Approved
0.6542 Remote Similarity NPD4838 Approved
0.6542 Remote Similarity NPD4836 Approved
0.6542 Remote Similarity NPD4837 Approved
0.6465 Remote Similarity NPD361 Discontinued
0.6449 Remote Similarity NPD2255 Approved
0.6422 Remote Similarity NPD7140 Approved
0.6422 Remote Similarity NPD7139 Approved
0.6422 Remote Similarity NPD7141 Clinical (unspecified phase)
0.6421 Remote Similarity NPD3160 Suspended
0.6417 Remote Similarity NPD4828 Approved
0.6417 Remote Similarity NPD4827 Approved
0.6417 Remote Similarity NPD4826 Approved
0.6404 Remote Similarity NPD2690 Discontinued
0.6355 Remote Similarity NPD881 Approved
0.6344 Remote Similarity NPD9034 Approved
0.6344 Remote Similarity NPD67 Phase 2
0.6321 Remote Similarity NPD7844 Discontinued
0.6214 Remote Similarity NPD618 Clinical (unspecified phase)
0.6148 Remote Similarity NPD6436 Phase 3
0.6071 Remote Similarity NPD1407 Approved
0.6034 Remote Similarity NPD8087 Discontinued
0.5926 Remote Similarity NPD8394 Approved
0.5882 Remote Similarity NPD3731 Phase 3
0.5785 Remote Similarity NPD4830 Approved
0.5785 Remote Similarity NPD4831 Approved
0.5785 Remote Similarity NPD4832 Approved
0.5784 Remote Similarity NPD882 Phase 2
0.5784 Remote Similarity NPD883 Phase 2
0.5729 Remote Similarity NPD6704 Discontinued
0.5726 Remote Similarity NPD8346 Approved
0.5726 Remote Similarity NPD8347 Approved
0.5726 Remote Similarity NPD8345 Approved
0.569 Remote Similarity NPD1428 Phase 2
0.5652 Remote Similarity NPD3161 Clinical (unspecified phase)
0.5648 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5641 Remote Similarity NPD8140 Approved
0.5641 Remote Similarity NPD8307 Discontinued
0.563 Remote Similarity NPD1805 Phase 2
0.563 Remote Similarity NPD1804 Phase 2

  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