NPASS Compound

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
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC314613

*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

Activity Type	# Activity
Ki	1
Others	2

Activity Type	# Activity
Others	3

Target ID	Target Type	Target Name	Activity Type	Activity Relation	Value	Unit	Reference
NPT27	Others	Unspecified	k cat	=	0.185	s-1	PMID[482301]
NPT27	Others	Unspecified	Km	=	2070000.0	nM	PMID[482301]
NPT27	Others	Unspecified	Ki	=	1140000.0	nM	PMID[482301]

☑ 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 NPC314613 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1535
0.1-0.2	15027
0.2-0.3	19323
0.3-0.4	6053
0.4-0.5	548
0.5-0.6	122
0.6-0.7	64
0.7-0.8	12
0.8-0.85	0
0.85-0.9	10
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.913	High Similarity	NPC325822
0.913	High Similarity	NPC61270
0.8605	High Similarity	NPC227707
0.8605	High Similarity	NPC99573
0.8605	High Similarity	NPC102981
0.8605	High Similarity	NPC111882
0.8605	High Similarity	NPC88278
0.8571	High Similarity	NPC321102
0.8571	High Similarity	NPC325153
0.8571	High Similarity	NPC322803
0.8571	High Similarity	NPC278465
0.7872	Intermediate Similarity	NPC207656
0.7872	Intermediate Similarity	NPC107091
0.7755	Intermediate Similarity	NPC188428
0.7755	Intermediate Similarity	NPC318700
0.7551	Intermediate Similarity	NPC88638
0.75	Intermediate Similarity	NPC174485
0.7442	Intermediate Similarity	NPC192065
0.7442	Intermediate Similarity	NPC86412
0.7442	Intermediate Similarity	NPC325034
0.7442	Intermediate Similarity	NPC293908
0.7442	Intermediate Similarity	NPC66052
0.7037	Intermediate Similarity	NPC314821
0.7037	Intermediate Similarity	NPC317501
0.7037	Intermediate Similarity	NPC317626
0.7021	Intermediate Similarity	NPC266553
0.6981	Remote Similarity	NPC329095
0.6852	Remote Similarity	NPC103672
0.6852	Remote Similarity	NPC320043
0.6744	Remote Similarity	NPC149070
0.6744	Remote Similarity	NPC127074
0.6744	Remote Similarity	NPC187058
0.6744	Remote Similarity	NPC182541
0.6744	Remote Similarity	NPC197207
0.66	Remote Similarity	NPC70756
0.66	Remote Similarity	NPC320240
0.6545	Remote Similarity	NPC476149
0.6545	Remote Similarity	NPC476136
0.6545	Remote Similarity	NPC300235
0.6545	Remote Similarity	NPC244869
0.6379	Remote Similarity	NPC3547
0.6364	Remote Similarity	NPC321873
0.6346	Remote Similarity	NPC21209
0.6346	Remote Similarity	NPC255377
0.6346	Remote Similarity	NPC176017
0.6346	Remote Similarity	NPC289758
0.6346	Remote Similarity	NPC73906
0.6346	Remote Similarity	NPC199857
0.6346	Remote Similarity	NPC285364
0.6346	Remote Similarity	NPC69445
0.6346	Remote Similarity	NPC92246
0.6346	Remote Similarity	NPC165846
0.6275	Remote Similarity	NPC29721
0.6226	Remote Similarity	NPC321087
0.6226	Remote Similarity	NPC277475
0.6182	Remote Similarity	NPC329128
0.6182	Remote Similarity	NPC322158
0.6167	Remote Similarity	NPC182903
0.6111	Remote Similarity	NPC14144
0.6071	Remote Similarity	NPC326533
0.6066	Remote Similarity	NPC323945
0.6047	Remote Similarity	NPC301586
0.6047	Remote Similarity	NPC325345
0.6047	Remote Similarity	NPC33415
0.6	Remote Similarity	NPC266566
0.6	Remote Similarity	NPC299781
0.6	Remote Similarity	NPC42503
0.6	Remote Similarity	NPC31433
0.6	Remote Similarity	NPC321170
0.6	Remote Similarity	NPC282143
0.6	Remote Similarity	NPC157193
0.5968	Remote Similarity	NPC320296
0.5926	Remote Similarity	NPC252918
0.5926	Remote Similarity	NPC230789
0.5902	Remote Similarity	NPC476209
0.5893	Remote Similarity	NPC323574
0.5862	Remote Similarity	NPC157514
0.5862	Remote Similarity	NPC130683
0.5862	Remote Similarity	NPC323361
0.5862	Remote Similarity	NPC107914
0.5862	Remote Similarity	NPC165198
0.5862	Remote Similarity	NPC242073
0.5862	Remote Similarity	NPC269166
0.5862	Remote Similarity	NPC58629
0.5862	Remote Similarity	NPC246558
0.5862	Remote Similarity	NPC89145
0.5862	Remote Similarity	NPC67660
0.5862	Remote Similarity	NPC145112
0.5818	Remote Similarity	NPC112363
0.5818	Remote Similarity	NPC247546
0.5818	Remote Similarity	NPC172086
0.5814	Remote Similarity	NPC320326
0.5789	Remote Similarity	NPC23134
0.5789	Remote Similarity	NPC124963
0.5789	Remote Similarity	NPC233726
0.5769	Remote Similarity	NPC317182
0.5769	Remote Similarity	NPC291502
0.5769	Remote Similarity	NPC86191
0.5769	Remote Similarity	NPC213159
0.5769	Remote Similarity	NPC298699
0.5769	Remote Similarity	NPC134252
0.5763	Remote Similarity	NPC327257
0.5763	Remote Similarity	NPC303727
0.5753	Remote Similarity	NPC317263
0.5714	Remote Similarity	NPC82512

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 NPC314613 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1751
0.1-0.2	5572
0.2-0.3	1330
0.3-0.4	344
0.4-0.5	76
0.5-0.6	41
0.6-0.7	28
0.7-0.8	5
0.8-0.85	0
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.913	High Similarity	NPD9061	Clinical (unspecified phase)
0.8605	High Similarity	NPD8995	Clinical (unspecified phase)
0.8605	High Similarity	NPD8996	Phase 3
0.7872	Intermediate Similarity	NPD9218	Clinical (unspecified phase)
0.7872	Intermediate Similarity	NPD9219	Approved
0.7755	Intermediate Similarity	NPD9065	Phase 3
0.7442	Intermediate Similarity	NPD9051	Approved
0.7442	Intermediate Similarity	NPD9052	Approved
0.7442	Intermediate Similarity	NPD9053	Approved
0.7308	Intermediate Similarity	NPD8991	Phase 1
0.7037	Intermediate Similarity	NPD9036	Phase 3
0.7037	Intermediate Similarity	NPD9035	Clinical (unspecified phase)
0.6852	Remote Similarity	NPD9049	Discontinued
0.6852	Remote Similarity	NPD9050	Approved
0.6744	Remote Similarity	NPD8814	Phase 3
0.6667	Remote Similarity	NPD8994	Approved
0.64	Remote Similarity	NPD8958	Phase 2
0.64	Remote Similarity	NPD8957	Approved
0.6346	Remote Similarity	NPD9000	Phase 3
0.6346	Remote Similarity	NPD8997	Approved
0.6346	Remote Similarity	NPD8993	Phase 1
0.6346	Remote Similarity	NPD8999	Phase 3
0.6346	Remote Similarity	NPD8998	Phase 2
0.6275	Remote Similarity	NPD9006	Approved
0.6111	Remote Similarity	NPD8965	Approved
0.6111	Remote Similarity	NPD8966	Approved
0.6071	Remote Similarity	NPD905	Approved
0.6071	Remote Similarity	NPD904	Phase 3
0.6047	Remote Similarity	NPD8988	Clinical (unspecified phase)
0.6047	Remote Similarity	NPD8549	Clinical (unspecified phase)
0.6	Remote Similarity	NPD8237	Approved
0.5918	Remote Similarity	NPD8977	Phase 3
0.5918	Remote Similarity	NPD8976	Approved
0.5862	Remote Similarity	NPD890	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD891	Phase 3
0.5862	Remote Similarity	NPD894	Approved
0.5862	Remote Similarity	NPD889	Approved
0.5862	Remote Similarity	NPD895	Approved
0.5862	Remote Similarity	NPD892	Phase 3
0.5862	Remote Similarity	NPD888	Phase 3
0.5862	Remote Similarity	NPD887	Approved
0.5862	Remote Similarity	NPD893	Approved
0.5818	Remote Similarity	NPD9139	Approved
0.5818	Remote Similarity	NPD9003	Clinical (unspecified phase)
0.5818	Remote Similarity	NPD9005	Phase 3
0.5818	Remote Similarity	NPD9004	Approved
0.5778	Remote Similarity	NPD8236	Phase 1
0.5778	Remote Similarity	NPD8234	Approved
0.5778	Remote Similarity	NPD8235	Approved
0.5769	Remote Similarity	NPD8788	Approved
0.569	Remote Similarity	NPD2269	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