Structure

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC313962

*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

☑ 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
NPT5885 Individual Protein Phospho-N-acetylmuramoyl-pentapeptide-transferase Escherichia coli K-12 IC50 = 0.01 ug.mL-1 PMID[491485]
NPT5885 Individual Protein Phospho-N-acetylmuramoyl-pentapeptide-transferase Escherichia coli K-12 IC50 = 0.01 ug.mL-1 PMID[491486]
NPT5885 Individual Protein Phospho-N-acetylmuramoyl-pentapeptide-transferase Escherichia coli K-12 IC50 = 17.0 nM PMID[491486]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 6.25 ug.mL-1 PMID[491485]
NPT1513 Organism Mycobacterium avium Mycobacterium avium MIC = 8.0 ug.mL-1 PMID[491485]
NPT86 Organism Mycobacterium intracellulare Mycobacterium intracellulare MIC = 4.0 ug.mL-1 PMID[491485]
NPT1828 Organism Mycobacterium kansasii Mycobacterium kansasii MIC = 16.0 ug.mL-1 PMID[491485]
NPT602 Organism Mycobacterium smegmatis Mycobacterium smegmatis MIC = 6.25 ug.mL-1 PMID[491486]
NPT1513 Organism Mycobacterium avium Mycobacterium avium MIC = 8.0 ug.mL-1 PMID[491486]
NPT86 Organism Mycobacterium intracellulare Mycobacterium intracellulare MIC = 4.0 ug.mL-1 PMID[491486]
NPT1828 Organism Mycobacterium kansasii Mycobacterium kansasii MIC = 16.0 ug.mL-1 PMID[491486]

☑ 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 NPC313962 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
0.9746 High Similarity NPC315058
0.7087 Intermediate Similarity NPC155087
0.7087 Intermediate Similarity NPC149843
0.6842 Remote Similarity NPC313813
0.6742 Remote Similarity NPC478024
0.6695 Remote Similarity NPC89051
0.6695 Remote Similarity NPC43246
0.6538 Remote Similarity NPC329277
0.6519 Remote Similarity NPC316244
0.6504 Remote Similarity NPC263545
0.6504 Remote Similarity NPC309898
0.6504 Remote Similarity NPC186840
0.6504 Remote Similarity NPC473950
0.6504 Remote Similarity NPC282705
0.6504 Remote Similarity NPC182632
0.6504 Remote Similarity NPC61894
0.6504 Remote Similarity NPC111567
0.6504 Remote Similarity NPC473581
0.6504 Remote Similarity NPC15851
0.6504 Remote Similarity NPC475125
0.6504 Remote Similarity NPC473604
0.6504 Remote Similarity NPC475603
0.65 Remote Similarity NPC325750
0.6452 Remote Similarity NPC36985
0.6452 Remote Similarity NPC17892
0.6441 Remote Similarity NPC106780
0.6424 Remote Similarity NPC247776
0.6424 Remote Similarity NPC475266
0.6424 Remote Similarity NPC475278
0.6424 Remote Similarity NPC304299
0.6424 Remote Similarity NPC309450
0.6423 Remote Similarity NPC242503
0.6423 Remote Similarity NPC139782
0.6423 Remote Similarity NPC74672
0.6423 Remote Similarity NPC43074
0.6423 Remote Similarity NPC209047
0.64 Remote Similarity NPC192066
0.64 Remote Similarity NPC73765
0.64 Remote Similarity NPC158445
0.64 Remote Similarity NPC70323
0.64 Remote Similarity NPC3568
0.64 Remote Similarity NPC283698
0.64 Remote Similarity NPC262312
0.64 Remote Similarity NPC157353
0.64 Remote Similarity NPC54961
0.64 Remote Similarity NPC35269
0.64 Remote Similarity NPC23454
0.64 Remote Similarity NPC256570
0.64 Remote Similarity NPC156782
0.64 Remote Similarity NPC282088
0.64 Remote Similarity NPC17290
0.6364 Remote Similarity NPC163352
0.6364 Remote Similarity NPC210456
0.6338 Remote Similarity NPC284651
0.6336 Remote Similarity NPC74035
0.6316 Remote Similarity NPC71866
0.6312 Remote Similarity NPC273185
0.6299 Remote Similarity NPC197294
0.6299 Remote Similarity NPC45313
0.6299 Remote Similarity NPC8098
0.6299 Remote Similarity NPC183449
0.6288 Remote Similarity NPC475918
0.626 Remote Similarity NPC55336
0.626 Remote Similarity NPC315063
0.6222 Remote Similarity NPC251122
0.621 Remote Similarity NPC324390
0.6183 Remote Similarity NPC477198
0.616 Remote Similarity NPC322594
0.616 Remote Similarity NPC320249
0.6131 Remote Similarity NPC314306
0.6129 Remote Similarity NPC171116
0.6127 Remote Similarity NPC245534
0.6119 Remote Similarity NPC315426
0.6116 Remote Similarity NPC71339
0.6116 Remote Similarity NPC228638
0.6116 Remote Similarity NPC112842
0.6045 Remote Similarity NPC201128
0.6 Remote Similarity NPC36254
0.6 Remote Similarity NPC318142
0.5974 Remote Similarity NPC315210
0.5974 Remote Similarity NPC315848
0.5971 Remote Similarity NPC241597
0.5959 Remote Similarity NPC471263
0.5951 Remote Similarity NPC477398
0.5944 Remote Similarity NPC470652
0.5938 Remote Similarity NPC318166
0.5938 Remote Similarity NPC324516
0.5933 Remote Similarity NPC314361
0.5923 Remote Similarity NPC475503
0.5906 Remote Similarity NPC327344
0.5891 Remote Similarity NPC317639
0.5887 Remote Similarity NPC296043
0.5879 Remote Similarity NPC321485
0.5879 Remote Similarity NPC317377
0.5862 Remote Similarity NPC20035
0.5845 Remote Similarity NPC329216
0.584 Remote Similarity NPC190334
0.584 Remote Similarity NPC62927
0.5833 Remote Similarity NPC328914
0.5827 Remote Similarity NPC29501
0.5798 Remote Similarity NPC329077
0.5782 Remote Similarity NPC470654
0.5782 Remote Similarity NPC470650
0.5782 Remote Similarity NPC470653
0.5772 Remote Similarity NPC163783
0.5759 Remote Similarity NPC142761
0.5758 Remote Similarity NPC475646
0.5753 Remote Similarity NPC471262
0.5753 Remote Similarity NPC469943
0.5735 Remote Similarity NPC189854
0.5735 Remote Similarity NPC166242
0.5735 Remote Similarity NPC322449
0.5735 Remote Similarity NPC92874
0.5735 Remote Similarity NPC62845
0.5734 Remote Similarity NPC6531
0.5714 Remote Similarity NPC471255
0.5714 Remote Similarity NPC476875
0.5714 Remote Similarity NPC315170
0.5693 Remote Similarity NPC10897
0.5693 Remote Similarity NPC325900
0.5689 Remote Similarity NPC319334
0.5689 Remote Similarity NPC327517
0.5689 Remote Similarity NPC322372
0.5687 Remote Similarity NPC477519
0.5685 Remote Similarity NPC160688
0.5685 Remote Similarity NPC315188
0.5682 Remote Similarity NPC328779
0.5667 Remote Similarity NPC470651
0.5667 Remote Similarity NPC470655
0.5664 Remote Similarity NPC30196
0.5662 Remote Similarity NPC476877
0.5662 Remote Similarity NPC314398
0.5662 Remote Similarity NPC239705
0.5662 Remote Similarity NPC314413
0.5649 Remote Similarity NPC226769
0.5649 Remote Similarity NPC280946
0.5649 Remote Similarity NPC6166
0.5649 Remote Similarity NPC471256
0.562 Remote Similarity NPC325902
0.561 Remote Similarity NPC471420
0.5608 Remote Similarity NPC50520
0.5606 Remote Similarity NPC120887
0.5606 Remote Similarity NPC90240
0.56 Remote Similarity NPC229249

  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 NPC313962 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
0.7083 Intermediate Similarity NPD7761 Suspended
0.6695 Remote Similarity NPD9580 Clinical (unspecified phase)
0.6695 Remote Similarity NPD9581 Clinical (unspecified phase)
0.6667 Remote Similarity NPD6935 Phase 3
0.6667 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6639 Remote Similarity NPD1686 Approved
0.6538 Remote Similarity NPD3129 Phase 3
0.6496 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6475 Remote Similarity NPD9565 Discontinued
0.6462 Remote Similarity NPD3128 Phase 3
0.6429 Remote Similarity NPD6436 Phase 3
0.6429 Remote Similarity NPD502 Approved
0.6423 Remote Similarity NPD8522 Clinical (unspecified phase)
0.64 Remote Similarity NPD9639 Clinical (unspecified phase)
0.6385 Remote Similarity NPD1407 Approved
0.6378 Remote Similarity NPD5789 Clinical (unspecified phase)
0.6364 Remote Similarity NPD241 Discontinued
0.635 Remote Similarity NPD3139 Phase 3
0.6333 Remote Similarity NPD9557 Clinical (unspecified phase)
0.6288 Remote Similarity NPD1385 Discontinued
0.6277 Remote Similarity NPD3138 Phase 3
0.626 Remote Similarity NPD841 Approved
0.626 Remote Similarity NPD755 Phase 3
0.6259 Remote Similarity NPD6918 Phase 1
0.6222 Remote Similarity NPD6421 Discontinued
0.6212 Remote Similarity NPD6946 Approved
0.619 Remote Similarity NPD501 Phase 1
0.6183 Remote Similarity NPD1061 Clinical (unspecified phase)
0.616 Remote Similarity NPD6943 Clinical (unspecified phase)
0.616 Remote Similarity NPD251 Approved
0.6131 Remote Similarity NPD7914 Suspended
0.6131 Remote Similarity NPD6430 Approved
0.6131 Remote Similarity NPD6429 Approved
0.6116 Remote Similarity NPD280 Approved
0.6115 Remote Similarity NPD869 Approved
0.6069 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6061 Remote Similarity NPD244 Clinical (unspecified phase)
0.6016 Remote Similarity NPD240 Phase 3
0.6 Remote Similarity NPD9558 Phase 3
0.6 Remote Similarity NPD4830 Approved
0.6 Remote Similarity NPD4832 Approved
0.6 Remote Similarity NPD4831 Approved
0.6 Remote Similarity NPD9556 Approved
0.5985 Remote Similarity NPD7651 Approved
0.5971 Remote Similarity NPD3731 Phase 3
0.5968 Remote Similarity NPD1760 Approved
0.595 Remote Similarity NPD9560 Approved
0.595 Remote Similarity NPD9561 Approved
0.5906 Remote Similarity NPD9585 Discontinued
0.5902 Remote Similarity NPD9546 Phase 2
0.5896 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5896 Remote Similarity NPD4743 Phase 2
0.5887 Remote Similarity NPD170 Approved
0.5854 Remote Similarity NPD239 Phase 2
0.5854 Remote Similarity NPD238 Clinical (unspecified phase)
0.5854 Remote Similarity NPD9533 Phase 2
0.5846 Remote Similarity NPD762 Discontinued
0.5845 Remote Similarity NPD7992 Clinical (unspecified phase)
0.584 Remote Similarity NPD9603 Phase 3
0.584 Remote Similarity NPD9604 Approved
0.584 Remote Similarity NPD9602 Phase 3
0.5833 Remote Similarity NPD1454 Phase 3
0.5833 Remote Similarity NPD1455 Phase 3
0.5799 Remote Similarity NPD5219 Approved
0.5799 Remote Similarity NPD5218 Approved
0.576 Remote Similarity NPD9562 Discovery
0.5758 Remote Similarity NPD192 Phase 2
0.5755 Remote Similarity NPD1804 Phase 2
0.5755 Remote Similarity NPD1805 Phase 2
0.5735 Remote Similarity NPD2700 Approved
0.5714 Remote Similarity NPD223 Clinical (unspecified phase)
0.5706 Remote Similarity NPD4521 Clinical (unspecified phase)
0.5693 Remote Similarity NPD1428 Phase 2
0.5691 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5682 Remote Similarity NPD6428 Approved
0.5645 Remote Similarity NPD9559 Phase 1
0.5645 Remote Similarity NPD9529 Phase 1
0.5615 Remote Similarity NPD279 Clinical (unspecified phase)
0.56 Remote Similarity NPD9601 Approved
0.56 Remote Similarity NPD205 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