Structure

Physi-Chem Properties

Molecular Weight:  672.36
Volume:  631.93
LogP:  -3.699
LogD:  -1.113
LogS:  -1.572
# Rotatable Bonds:  21
TPSA:  334.55
# H-Bond Aceptor:  20
# H-Bond Donor:  16
# Rings:  3
# Heavy Atoms:  20

MedChem Properties

QED Drug-Likeness Score:  0.07
Synthetic Accessibility Score:  5.448
Fsp3:  0.741
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.091
MDCK Permeability:  1.8299682778888382e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.998
Human Intestinal Absorption (HIA):  0.983
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.432
Plasma Protein Binding (PPB):  14.492655754089355%
Volume Distribution (VD):  0.327
Pgp-substrate:  76.70935821533203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.007
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.035
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.004
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.062
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.017

ADMET: Excretion

Clearance (CL):  1.253
Half-life (T1/2):  0.648

ADMET: Toxicity

hERG Blockers:  0.087
Human Hepatotoxicity (H-HT):  0.235
Drug-inuced Liver Injury (DILI):  0.039
AMES Toxicity:  0.146
Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.974
Skin Sensitization:  0.111
Carcinogencity:  0.032
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.06

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

  Natural Product: NPC189854

Natural Product ID:  NPC189854
Common Name*:   (2S,3S,4R)-10-De-O-Carbamoyl-12-O-Carbamoyl-Nbeta-Acetyl 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-acetamido-6-[[(3S)-3,6-diaminohexanoyl]amino]hexanoyl]amino]-3,4-dihydroxyoxan-2-yl]methyl carbamate
Synonyms:  
Standard InCHIKey:  WJRALRAIXBIBCJ-IVVRDDJBSA-N
Standard InCHI:  InChI=1S/C27H48N10O10/c1-12(38)33-14(5-3-7-31-17(40)8-13(29)4-2-6-28)9-18(41)34-21-23(43)22(42)16(11-46-26(30)45)47-25(21)37-27-35-19-15(39)10-32-24(44)20(19)36-27/h13-16,19-23,25,39,42-43H,2-11,28-29H2,1H3,(H2,30,45)(H,31,40)(H,32,44)(H,33,38)(H,34,41)(H2,35,36,37)/t13-,14-,15+,16+,19+,20-,21+,22-,23-,25+/m0/s1
SMILES:  NCCC[C@@H](CC(=NCCC[C@@H](CC(=N[C@H]1[C@H](NC2=N[C@H]3[C@H](N2)C(=NC[C@H]3O)O)O[C@@H]([C@@H]([C@H]1O)O)COC(=N)O)O)N=C(O)C)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2088424
PubChem CID:   70693300
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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 256.0 ug.mL-1 PMID[502365]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 256.0 ug.mL-1 PMID[502365]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 128.0 ug.mL-1 PMID[502365]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC > 256.0 ug.mL-1 PMID[502365]
NPT1107 Organism Mycobacterium smegmatis str. MC2 155 Mycobacterium smegmatis str. MC2 155 MIC > 256.0 ug.mL-1 PMID[502365]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 256.0 ug.mL-1 PMID[502365]
NPT3495 Organism Morganella morganii Morganella morganii MIC > 256.0 ug.mL-1 PMID[502365]
NPT19 Organism Escherichia coli Escherichia coli MIC > 256.0 ug.mL-1 PMID[502365]
NPT20 Organism Candida albicans Candida albicans MIC > 256.0 ug.mL-1 PMID[502365]

☑ 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 NPC189854 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 NPC62845
1.0 High Similarity NPC92874
1.0 High Similarity NPC166242
1.0 High Similarity NPC322449
0.9897 High Similarity NPC325900
0.9897 High Similarity NPC10897
0.9896 High Similarity NPC314398
0.9896 High Similarity NPC239705
0.9896 High Similarity NPC314413
0.8611 High Similarity NPC259586
0.8532 High Similarity NPC470621
0.8532 High Similarity NPC222481
0.6983 Remote Similarity NPC57436
0.6983 Remote Similarity NPC121479
0.6833 Remote Similarity NPC313813
0.6697 Remote Similarity NPC216278
0.6441 Remote Similarity NPC59589
0.6429 Remote Similarity NPC330590
0.6378 Remote Similarity NPC94319
0.6311 Remote Similarity NPC316807
0.63 Remote Similarity NPC315806
0.6296 Remote Similarity NPC306838
0.6214 Remote Similarity NPC314772
0.6214 Remote Similarity NPC314968
0.6207 Remote Similarity NPC315036
0.6095 Remote Similarity NPC318258
0.6095 Remote Similarity NPC83248
0.6095 Remote Similarity NPC100204
0.6095 Remote Similarity NPC70574
0.6091 Remote Similarity NPC214376
0.6075 Remote Similarity NPC165119
0.6068 Remote Similarity NPC471628
0.6068 Remote Similarity NPC56298
0.6031 Remote Similarity NPC477518
0.6018 Remote Similarity NPC328646
0.6 Remote Similarity NPC327753
0.6 Remote Similarity NPC327486
0.6 Remote Similarity NPC98750
0.6 Remote Similarity NPC223174
0.6 Remote Similarity NPC313552
0.5982 Remote Similarity NPC176381
0.5982 Remote Similarity NPC195969
0.5981 Remote Similarity NPC242077
0.5981 Remote Similarity NPC36927
0.5981 Remote Similarity NPC271772
0.5962 Remote Similarity NPC329077
0.5954 Remote Similarity NPC325750
0.5946 Remote Similarity NPC328806
0.5946 Remote Similarity NPC314408
0.5946 Remote Similarity NPC314007
0.5946 Remote Similarity NPC123746
0.5946 Remote Similarity NPC43850
0.5946 Remote Similarity NPC477060
0.5922 Remote Similarity NPC474467
0.5912 Remote Similarity NPC318142
0.5856 Remote Similarity NPC62927
0.5856 Remote Similarity NPC190334
0.5847 Remote Similarity NPC328914
0.5826 Remote Similarity NPC315334
0.578 Remote Similarity NPC263058
0.5766 Remote Similarity NPC469363
0.5758 Remote Similarity NPC139857
0.5758 Remote Similarity NPC471262
0.5755 Remote Similarity NPC325902
0.5752 Remote Similarity NPC470284
0.5752 Remote Similarity NPC275715
0.5746 Remote Similarity NPC315058
0.5741 Remote Similarity NPC471420
0.5739 Remote Similarity NPC270005
0.5739 Remote Similarity NPC208537
0.5735 Remote Similarity NPC313962
0.5726 Remote Similarity NPC90240
0.57 Remote Similarity NPC129100
0.57 Remote Similarity NPC291650
0.57 Remote Similarity NPC322801
0.5688 Remote Similarity NPC315969
0.5686 Remote Similarity NPC319334
0.5686 Remote Similarity NPC321485
0.5686 Remote Similarity NPC322372
0.5686 Remote Similarity NPC327517
0.5686 Remote Similarity NPC317377
0.5682 Remote Similarity NPC245534
0.5678 Remote Similarity NPC328779
0.5678 Remote Similarity NPC313821
0.5672 Remote Similarity NPC68327
0.5672 Remote Similarity NPC75839
0.5664 Remote Similarity NPC470282
0.5656 Remote Similarity NPC221148
0.5644 Remote Similarity NPC316445
0.5641 Remote Similarity NPC280946
0.5641 Remote Similarity NPC226769
0.5641 Remote Similarity NPC6166
0.5631 Remote Similarity NPC476694
0.5631 Remote Similarity NPC476695
0.5631 Remote Similarity NPC476696
0.563 Remote Similarity NPC471263
0.5625 Remote Similarity NPC241597
0.56 Remote Similarity NPC155087
0.56 Remote Similarity NPC315980
0.56 Remote Similarity NPC149843

  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 NPC189854 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
0.6983 Remote Similarity NPD4833 Approved
0.6983 Remote Similarity NPD35 Approved
0.6944 Remote Similarity NPD6424 Approved
0.6903 Remote Similarity NPD8045 Clinical (unspecified phase)
0.69 Remote Similarity NPD9429 Discontinued
0.6897 Remote Similarity NPD284 Phase 1
0.6765 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6697 Remote Similarity NPD6426 Approved
0.6697 Remote Similarity NPD6423 Approved
0.6697 Remote Similarity NPD6425 Approved
0.6697 Remote Similarity NPD6427 Approved
0.6667 Remote Similarity NPD6432 Approved
0.6667 Remote Similarity NPD6433 Approved
0.6667 Remote Similarity NPD6431 Approved
0.6667 Remote Similarity NPD6434 Clinical (unspecified phase)
0.6638 Remote Similarity NPD5376 Approved
0.6429 Remote Similarity NPD5381 Approved
0.6429 Remote Similarity NPD5378 Approved
0.6429 Remote Similarity NPD5377 Approved
0.6378 Remote Similarity NPD4827 Approved
0.6378 Remote Similarity NPD4826 Approved
0.6378 Remote Similarity NPD4828 Approved
0.6372 Remote Similarity NPD6428 Approved
0.6341 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6337 Remote Similarity NPD9407 Approved
0.63 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6273 Remote Similarity NPD3716 Discontinued
0.6262 Remote Similarity NPD9654 Phase 2
0.6214 Remote Similarity NPD9434 Approved
0.6214 Remote Similarity NPD9435 Approved
0.6174 Remote Similarity NPD4282 Approved
0.616 Remote Similarity NPD869 Approved
0.6107 Remote Similarity NPD4816 Clinical (unspecified phase)
0.61 Remote Similarity NPD5386 Phase 2
0.6091 Remote Similarity NPD2698 Approved
0.6071 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6068 Remote Similarity NPD4838 Approved
0.6068 Remote Similarity NPD4835 Approved
0.6068 Remote Similarity NPD4836 Approved
0.6068 Remote Similarity NPD4837 Approved
0.6061 Remote Similarity NPD3213 Discontinued
0.604 Remote Similarity NPD9405 Approved
0.6016 Remote Similarity NPD1805 Phase 2
0.6016 Remote Similarity NPD1804 Phase 2
0.6 Remote Similarity NPD2700 Approved
0.6 Remote Similarity NPD6946 Approved
0.6 Remote Similarity NPD6436 Phase 3
0.6 Remote Similarity NPD9445 Approved
0.6 Remote Similarity NPD7844 Discontinued
0.5982 Remote Similarity NPD5796 Clinical (unspecified phase)
0.5982 Remote Similarity NPD5795 Approved
0.5982 Remote Similarity NPD5797 Approved
0.5982 Remote Similarity NPD5794 Approved
0.5982 Remote Similarity NPD5798 Approved
0.5981 Remote Similarity NPD9646 Approved
0.5981 Remote Similarity NPD9644 Approved
0.5981 Remote Similarity NPD9645 Approved
0.5966 Remote Similarity NPD1061 Clinical (unspecified phase)
0.595 Remote Similarity NPD1428 Phase 2
0.5946 Remote Similarity NPD3202 Approved
0.5946 Remote Similarity NPD3207 Approved
0.5946 Remote Similarity NPD3201 Approved
0.5946 Remote Similarity NPD3208 Approved
0.5946 Remote Similarity NPD3203 Approved
0.5946 Remote Similarity NPD3209 Approved
0.5929 Remote Similarity NPD9585 Discontinued
0.5929 Remote Similarity NPD285 Discontinued
0.5856 Remote Similarity NPD9602 Phase 3
0.5856 Remote Similarity NPD9604 Approved
0.5856 Remote Similarity NPD3200 Clinical (unspecified phase)
0.5856 Remote Similarity NPD9603 Phase 3
0.5847 Remote Similarity NPD1454 Phase 3
0.5847 Remote Similarity NPD1455 Phase 3
0.5847 Remote Similarity NPD223 Clinical (unspecified phase)
0.5842 Remote Similarity NPD2702 Phase 1
0.5842 Remote Similarity NPD2704 Phase 3
0.5785 Remote Similarity NPD4743 Phase 2
0.578 Remote Similarity NPD4829 Discontinued
0.5758 Remote Similarity NPD2703 Discontinued
0.5714 Remote Similarity NPD1760 Approved
0.57 Remote Similarity NPD9033 Approved
0.57 Remote Similarity NPD374 Approved
0.57 Remote Similarity NPD373 Approved
0.57 Remote Similarity NPD9031 Approved
0.57 Remote Similarity NPD9032 Approved
0.57 Remote Similarity NPD9030 Approved
0.5691 Remote Similarity NPD1385 Discontinued
0.568 Remote Similarity NPD6941 Approved
0.5678 Remote Similarity NPD3191 Approved
0.5678 Remote Similarity NPD3189 Approved
0.5678 Remote Similarity NPD3190 Approved
0.5672 Remote Similarity NPD577 Phase 3
0.5672 Remote Similarity NPD591 Approved
0.5659 Remote Similarity NPD4832 Approved
0.5659 Remote Similarity NPD4831 Approved
0.5659 Remote Similarity NPD4830 Approved
0.5656 Remote Similarity NPD1449 Approved
0.5656 Remote Similarity NPD1450 Approved
0.5625 Remote Similarity NPD3731 Phase 3
0.562 Remote Similarity NPD7651 Approved
0.56 Remote Similarity NPD877 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