NPASS Compound

Structure

CID315110 OpenBabel06191716132D 41 45 0 0 1 0 0 0 0 0999 V2000 -6.6112 -1.9069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6527 -0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4804 -6.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0002 -1.9086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4379 -3.3381 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8265 1.4310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0007 -2.8627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3056 -1.9076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6533 -4.7705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3063 -4.7704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7851 -2.3842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8264 -0.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3068 -6.6786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1322 -2.3846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 -1.9087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8268 -3.3395 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4792 -2.3850 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6532 -3.8164 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3060 -3.8163 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1324 -3.3389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8267 -1.4314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6528 -1.9081 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9585 -1.9072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8263 -1.4316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9590 -3.8159 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8265 -0.4770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7853 -3.3385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1329 -6.2013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8271 -5.2476 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.1327 -5.2472 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8267 -2.3855 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.4795 -3.3393 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -3.3070 -7.6326 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9583 -0.9532 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6524 -1.9088 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9592 -4.7700 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6527 0.0001 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9593 -6.6781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6117 -3.8154 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 0.9541 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 11 1 0 0 0 0 2 12 1 0 0 0 0 3 13 1 0 0 0 0 4 32 1 0 0 0 0 5 40 1 0 0 0 0 6 41 1 0 0 0 0 7 15 1 0 0 0 0 8 14 1 0 0 0 0 8 17 1 0 0 0 0 9 18 1 0 0 0 0 9 30 3 0 0 0 0 10 19 1 0 0 0 0 10 31 1 0 0 0 0 11 23 1 0 0 0 0 11 27 2 0 0 0 0 12 24 1 0 0 0 0 12 28 2 0 0 0 0 13 29 1 0 0 0 0 13 34 2 0 0 0 0 14 20 2 0 0 0 0 14 23 1 0 0 0 0 15 21 2 0 0 0 0 15 24 1 0 0 0 0 16 7 1 1 0 0 0 16 18 1 0 0 0 0 16 32 1 0 0 0 0 17 22 1 0 0 0 0 17 33 1 1 0 0 0 18 33 1 6 0 0 0 19 20 1 0 0 0 0 19 33 1 1 0 0 0 20 25 1 0 0 0 0 21 26 1 0 0 0 0 22 21 1 1 0 0 0 22 32 1 0 0 0 0 23 35 2 0 0 0 0 24 36 2 0 0 0 0 25 27 1 0 0 0 0 25 37 2 0 0 0 0 26 28 1 0 0 0 0 26 38 2 0 0 0 0 27 40 1 0 0 0 0 28 41 1 0 0 0 0 29 31 1 0 0 0 0 29 39 2 0 0 0 0 M END $$$$

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Download Data

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

Natural Product: NPC315110

*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
IC50	14

Activity Type	# Activity
Cell Line	12
NON-MOLECULAR	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	0.4	nM	PMID[479218]
NPT3558	Cell Line	QG-56		IC50	=	5.5	nM	PMID[479218]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	2.1	nM	PMID[479218]
NPT579	Cell Line	DLD-1	Homo sapiens	IC50	=	0.6	nM	PMID[479218]
NPT180	Cell Line	HCT-8	Homo sapiens	IC50	=	2.49	nM	PMID[479219]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	=	1.83	nM	PMID[479219]
NPT1085	Cell Line	KETR3	Homo sapiens	IC50	=	9.56	nM	PMID[479219]
NPT179	Cell Line	A2780	Homo sapiens	IC50	=	2.75	nM	PMID[479219]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	6.39	nM	PMID[479219]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	40.44	nM	PMID[479219]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	1.06	nM	PMID[479219]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	2.23	nM	PMID[479219]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	10.98	nM	PMID[479219]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	2.54	nM	PMID[479219]

☑ 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 NPC315110 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	140
0.1-0.2	1812
0.2-0.3	25645
0.3-0.4	13478
0.4-0.5	1526
0.5-0.6	84
0.6-0.7	5
0.7-0.8	5
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.7538	Intermediate Similarity	NPC97861
0.7424	Intermediate Similarity	NPC161644
0.7259	Intermediate Similarity	NPC239252
0.7259	Intermediate Similarity	NPC473703
0.7174	Intermediate Similarity	NPC473955
0.705	Intermediate Similarity	NPC25025
0.6812	Remote Similarity	NPC475987
0.6812	Remote Similarity	NPC313348
0.6794	Remote Similarity	NPC13351
0.6134	Remote Similarity	NPC116231
0.6094	Remote Similarity	NPC87919
0.6084	Remote Similarity	NPC315011
0.5966	Remote Similarity	NPC472161
0.575	Remote Similarity	NPC475614
0.5714	Remote Similarity	NPC139867
0.5705	Remote Similarity	NPC82129
0.5645	Remote Similarity	NPC236322

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 NPC315110 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	107
0.1-0.2	761
0.2-0.3	4571
0.3-0.4	3362
0.4-0.5	332
0.5-0.6	16
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD7196	Clinical (unspecified phase)
0.6084	Remote Similarity	NPD2101	Approved
0.5714	Remote Similarity	NPD1689	Approved
0.5643	Remote Similarity	NPD2132	Phase 3

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