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: NPC315063

*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
NPT2971 Individual Protein DNA dC->dU-editing enzyme APOBEC-3F Homo sapiens Potency n.a. 35481.3 nM PMID[487775]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 18356.4 nM PMID[487775]
NPT477 Individual Protein DNA dC->dU-editing enzyme APOBEC-3G Homo sapiens Potency n.a. 2511.9 nM PMID[487775]
NPT478 Individual Protein Ataxin-2 Homo sapiens Potency n.a. 39810.7 nM PMID[487775]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 18356.4 nM PMID[487775]
NPT50 Individual Protein Tyrosyl-DNA phosphodiesterase 1 Homo sapiens Potency n.a. 23109.3 nM PMID[487775]
NPT444 Individual Protein Ubiquitin carboxyl-terminal hydrolase 1 Homo sapiens Potency n.a. 35481.3 nM PMID[487775]
NPT535 Individual Protein Parathyroid hormone receptor Homo sapiens Potency n.a. 7943.3 nM PMID[487775]
NPT2 Others Unspecified IC50 = 12410.0 nM PMID[487775]
NPT2 Others Unspecified IC50 = 28550.0 nM PMID[487775]
NPT2 Others Unspecified EC50 = 16320.0 nM PMID[487775]
NPT2 Others Unspecified IC50 = 1735.0 nM PMID[487775]
NPT2 Others Unspecified Potency n.a. 1995.3 nM PMID[487775]
NPT2 Others Unspecified Potency n.a. 501.2 nM PMID[487775]
NPT861 Individual Protein Isocitrate dehydrogenase [NADP] cytoplasmic Homo sapiens Potency n.a. 20596.2 nM PMID[487775]

☑ 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 NPC315063 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
0.9167 High Similarity NPC43246
0.9167 High Similarity NPC89051
0.881 High Similarity NPC106780
0.8462 Intermediate Similarity NPC17892
0.8462 Intermediate Similarity NPC36985
0.837 Intermediate Similarity NPC283698
0.837 Intermediate Similarity NPC73765
0.8202 Intermediate Similarity NPC210456
0.8202 Intermediate Similarity NPC163352
0.8132 Intermediate Similarity NPC324390
0.8095 Intermediate Similarity NPC329077
0.8043 Intermediate Similarity NPC320249
0.8043 Intermediate Similarity NPC322594
0.7865 Intermediate Similarity NPC71339
0.7865 Intermediate Similarity NPC112842
0.7802 Intermediate Similarity NPC62927
0.7802 Intermediate Similarity NPC190334
0.7604 Intermediate Similarity NPC317639
0.7549 Intermediate Similarity NPC329277
0.7473 Intermediate Similarity NPC229249
0.7447 Intermediate Similarity NPC171116
0.7404 Intermediate Similarity NPC155087
0.7404 Intermediate Similarity NPC149843
0.7386 Intermediate Similarity NPC325902
0.7292 Intermediate Similarity NPC327344
0.7245 Intermediate Similarity NPC226769
0.7245 Intermediate Similarity NPC6166
0.7245 Intermediate Similarity NPC280946
0.7172 Intermediate Similarity NPC120887
0.7172 Intermediate Similarity NPC90240
0.7143 Intermediate Similarity NPC318166
0.7143 Intermediate Similarity NPC324516
0.71 Intermediate Similarity NPC328779
0.6979 Remote Similarity NPC328806
0.6961 Remote Similarity NPC328914
0.6882 Remote Similarity NPC319753
0.6842 Remote Similarity NPC325723
0.68 Remote Similarity NPC329384
0.6742 Remote Similarity NPC315806
0.6471 Remote Similarity NPC284651
0.6417 Remote Similarity NPC315058
0.64 Remote Similarity NPC109188
0.6372 Remote Similarity NPC478024
0.626 Remote Similarity NPC313962
0.5984 Remote Similarity NPC325750
0.5895 Remote Similarity NPC470782
0.5851 Remote Similarity NPC126186
0.5798 Remote Similarity NPC313813
0.5729 Remote Similarity NPC469972

  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 NPC315063 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
0.9167 High Similarity NPD9580 Clinical (unspecified phase)
0.9167 High Similarity NPD9581 Clinical (unspecified phase)
0.8605 High Similarity NPD9557 Clinical (unspecified phase)
0.8506 High Similarity NPD9562 Discovery
0.837 Intermediate Similarity NPD9639 Clinical (unspecified phase)
0.814 Intermediate Similarity NPD9556 Approved
0.8132 Intermediate Similarity NPD9565 Discontinued
0.8046 Intermediate Similarity NPD9561 Approved
0.8046 Intermediate Similarity NPD9560 Approved
0.8022 Intermediate Similarity NPD755 Phase 3
0.7957 Intermediate Similarity NPD1686 Approved
0.7955 Intermediate Similarity NPD9546 Phase 2
0.7955 Intermediate Similarity NPD9559 Phase 1
0.7931 Intermediate Similarity NPD9558 Phase 3
0.7865 Intermediate Similarity NPD9533 Phase 2
0.7865 Intermediate Similarity NPD280 Approved
0.7812 Intermediate Similarity NPD502 Approved
0.7802 Intermediate Similarity NPD9603 Phase 3
0.7802 Intermediate Similarity NPD241 Discontinued
0.7802 Intermediate Similarity NPD9602 Phase 3
0.7802 Intermediate Similarity NPD9604 Approved
0.7708 Intermediate Similarity NPD762 Discontinued
0.7692 Intermediate Similarity NPD240 Phase 3
0.7692 Intermediate Similarity NPD170 Approved
0.7624 Intermediate Similarity NPD3128 Phase 3
0.7556 Intermediate Similarity NPD9529 Phase 1
0.7549 Intermediate Similarity NPD3129 Phase 3
0.75 Intermediate Similarity NPD501 Phase 1
0.7475 Intermediate Similarity NPD223 Clinical (unspecified phase)
0.7474 Intermediate Similarity NPD9585 Discontinued
0.7474 Intermediate Similarity NPD6943 Clinical (unspecified phase)
0.7473 Intermediate Similarity NPD9601 Approved
0.7473 Intermediate Similarity NPD238 Clinical (unspecified phase)
0.7473 Intermediate Similarity NPD239 Phase 2
0.7447 Intermediate Similarity NPD841 Approved
0.7419 Intermediate Similarity NPD1760 Approved
0.7292 Intermediate Similarity NPD251 Approved
0.7255 Intermediate Similarity NPD1061 Clinical (unspecified phase)
0.7172 Intermediate Similarity NPD514 Clinical (unspecified phase)
0.7158 Intermediate Similarity NPD9554 Approved
0.7158 Intermediate Similarity NPD9553 Approved
0.7158 Intermediate Similarity NPD301 Discontinued
0.7157 Intermediate Similarity NPD7651 Approved
0.7143 Intermediate Similarity NPD9600 Approved
0.7041 Intermediate Similarity NPD279 Clinical (unspecified phase)
0.701 Intermediate Similarity NPD267 Discontinued
0.7 Intermediate Similarity NPD3138 Phase 3
0.6989 Remote Similarity NPD9572 Clinical (unspecified phase)
0.6972 Remote Similarity NPD7914 Suspended
0.6961 Remote Similarity NPD1454 Phase 3
0.6961 Remote Similarity NPD1455 Phase 3
0.6937 Remote Similarity NPD3139 Phase 3
0.6887 Remote Similarity NPD1385 Discontinued
0.6882 Remote Similarity NPD9573 Phase 2
0.6863 Remote Similarity NPD5789 Clinical (unspecified phase)
0.68 Remote Similarity NPD215 Discontinued
0.6742 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9555 Phase 2
0.6667 Remote Similarity NPD9429 Discontinued
0.6636 Remote Similarity NPD6946 Approved
0.6593 Remote Similarity NPD9407 Approved
0.6542 Remote Similarity NPD2633 Phase 1
0.6538 Remote Similarity NPD192 Phase 2
0.65 Remote Similarity NPD500 Discontinued
0.6486 Remote Similarity NPD1805 Phase 2
0.6486 Remote Similarity NPD1804 Phase 2
0.6422 Remote Similarity NPD1428 Phase 2
0.64 Remote Similarity NPD1331 Approved
0.6389 Remote Similarity NPD4743 Phase 2
0.6354 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6306 Remote Similarity NPD6693 Phase 3
0.6279 Remote Similarity NPD9503 Approved
0.6279 Remote Similarity NPD9504 Approved
0.6264 Remote Similarity NPD9405 Approved
0.6226 Remote Similarity NPD3121 Phase 2
0.6154 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6935 Phase 3
0.6117 Remote Similarity NPD285 Discontinued
0.6017 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6 Remote Similarity NPD1706 Clinical (unspecified phase)
0.5966 Remote Similarity NPD7756 Clinical (unspecified phase)
0.59 Remote Similarity NPD205 Approved
0.5872 Remote Similarity NPD765 Discontinued
0.5789 Remote Similarity NPD7761 Suspended
0.5729 Remote Similarity NPD9370 Approved
0.5714 Remote Similarity NPD244 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9427 Approved
0.5714 Remote Similarity NPD9369 Clinical (unspecified phase)
0.5702 Remote Similarity NPD6918 Phase 1
0.5648 Remote Similarity NPD6948 Phase 3
0.5612 Remote Similarity NPD9372 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