NPASS Compound

Structure

CID216278 OpenBabel06191716002D 48 49 0 0 1 0 0 0 0 0999 V2000 -5.9845 -6.0109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0376 -5.6894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1796 -6.9917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5944 -4.0493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6401 -0.5567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9560 -1.4284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4766 4.0477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4355 4.0477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9505 0.3902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8425 -4.7087 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9616 0.3902 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9560 -1.4284 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0321 3.2163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8799 3.2163 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.9697 0.5853 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3993 -3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6593 -0.7518 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9424 0.5853 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.8799 -1.0457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3250 2.5092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9560 3.5989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9697 1.5853 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3250 -0.3386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3214 0.9469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3633 5.7761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1266 -7.3131 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.8956 -4.3872 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.3379 1.6988 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.3654 5.7107 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.0321 -1.0457 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.9189 4.9446 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.1511 -2.4092 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9560 3.5989 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.5870 -0.3386 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.5870 2.5092 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.3022 1.1420 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9424 1.5853 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.9932 4.9446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.6098 1.1420 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4523 -2.7471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3379 -1.6988 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4355 -1.8772 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4936 3.0647 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1511 4.5797 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.9505 1.7804 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4936 -0.8942 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8056 6.6729 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 2 10 1 0 0 0 0 3 26 1 0 0 0 0 4 10 1 0 0 0 0 4 16 1 0 0 0 0 5 17 1 0 0 0 0 6 12 1 0 0 0 0 6 30 1 0 0 0 0 7 13 2 0 0 0 0 7 31 1 0 0 0 0 8 39 1 0 0 0 0 9 40 1 0 0 0 0 10 27 1 1 0 0 0 11 5 1 6 0 0 0 11 18 1 0 0 0 0 11 36 1 0 0 0 0 12 19 1 0 0 0 0 12 32 1 6 0 0 0 13 20 1 0 0 0 0 13 33 1 0 0 0 0 14 8 1 1 0 0 0 14 21 1 0 0 0 0 14 35 1 0 0 0 0 15 9 1 1 0 0 0 15 22 1 0 0 0 0 15 34 1 0 0 0 0 16 32 2 3 0 0 0 16 41 1 0 0 0 0 17 37 1 0 0 0 0 17 42 1 1 0 0 0 18 23 1 1 0 0 0 18 38 1 0 0 0 0 19 34 2 3 0 0 0 19 43 1 0 0 0 0 20 38 2 3 0 0 0 20 44 1 0 0 0 0 21 33 2 3 0 0 0 21 45 1 0 0 0 0 22 35 2 3 0 0 0 22 46 1 0 0 0 0 23 30 2 3 0 0 0 23 47 1 0 0 0 0 24 28 2 0 0 0 0 24 36 1 0 0 0 0 24 37 1 0 0 0 0 25 29 2 0 0 0 0 25 31 1 0 0 0 0 25 48 1 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

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

Natural Product: NPC216278

*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	2
Kd	1
Others	7

Activity Type	# Activity
Individual Protein	2
ORGANISM	2
PROTEIN NUCLEIC-ACID COMPLEX	168
Uncleic Acid	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT12	Individual Protein	Human immunodeficiency virus type 1 integrase	Human immunodeficiency virus 1	Inhibition	<	50.0	%	PMID[481700]
NPT317	Uncleic Acid	Nucleic Acid		Kd	<	3000.0	nM	PMID[481701]
NPT25608	PROTEIN NUCLEIC-ACID COMPLEX	Bacterial 70S ribosome	Bacteria	Activity	=	10.0	%	PMID[481702]
NPT25608	PROTEIN NUCLEIC-ACID COMPLEX	Bacterial 70S ribosome	Bacteria	FC	=	1.5	n.a.	PMID[481702]
NPT25608	PROTEIN NUCLEIC-ACID COMPLEX	Bacterial 70S ribosome	Bacteria	FC	=	2.0	n.a.	PMID[481702]
NPT317	Uncleic Acid	Nucleic Acid		Activity	=	46.8	%	PMID[481702]
NPT317	Uncleic Acid	Nucleic Acid		Activity	=	0.04	/s	PMID[481702]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	20000.0	nM	PMID[481704]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	19952.62	nM	PMID[481704]

☑ 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 NPC216278 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	186
0.1-0.2	19451
0.2-0.3	19130
0.3-0.4	3026
0.4-0.5	793
0.5-0.6	96
0.6-0.7	14
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	Natural Product ID
0.6759	Remote Similarity	NPC239705
0.6759	Remote Similarity	NPC314413
0.6759	Remote Similarity	NPC314398
0.6697	Remote Similarity	NPC166242
0.6697	Remote Similarity	NPC322449
0.6697	Remote Similarity	NPC92874
0.6697	Remote Similarity	NPC62845
0.6697	Remote Similarity	NPC189854
0.6636	Remote Similarity	NPC10897
0.6636	Remote Similarity	NPC325900
0.6429	Remote Similarity	NPC242077
0.6186	Remote Similarity	NPC259586
0.6134	Remote Similarity	NPC222481
0.6134	Remote Similarity	NPC470621
0.6	Remote Similarity	NPC313813
0.5806	Remote Similarity	NPC323762
0.5729	Remote Similarity	NPC328457
0.57	Remote Similarity	NPC191774
0.5673	Remote Similarity	NPC229249
0.566	Remote Similarity	NPC190334
0.566	Remote Similarity	NPC62927

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 NPC216278 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	80
0.1-0.2	1372
0.2-0.3	5608
0.3-0.4	1770
0.4-0.5	277
0.5-0.6	29
0.6-0.7	4
0.7-0.8	1
0.8-0.85	0
0.85-0.9	1
0.9-0.95	3
0.95-1	5

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD6426	Approved
1.0	High Similarity	NPD6425	Approved
1.0	High Similarity	NPD6427	Approved
1.0	High Similarity	NPD6423	Approved
0.9767	High Similarity	NPD6434	Clinical (unspecified phase)
0.9767	High Similarity	NPD6431	Approved
0.9767	High Similarity	NPD6433	Approved
0.9767	High Similarity	NPD6432	Approved
0.9438	High Similarity	NPD6424	Approved
0.7159	Intermediate Similarity	NPD5386	Phase 2
0.6429	Remote Similarity	NPD9645	Approved
0.6429	Remote Similarity	NPD9646	Approved
0.6429	Remote Similarity	NPD9644	Approved
0.6316	Remote Similarity	NPD284	Phase 1
0.6304	Remote Similarity	NPD2702	Phase 1
0.6304	Remote Similarity	NPD2704	Phase 3
0.6238	Remote Similarity	NPD9654	Phase 2
0.6207	Remote Similarity	NPD1155	Discontinued
0.604	Remote Similarity	NPD4829	Discontinued
0.5789	Remote Similarity	NPD1061	Clinical (unspecified phase)
0.5741	Remote Similarity	NPD9585	Discontinued
0.5738	Remote Similarity	NPD869	Approved
0.5703	Remote Similarity	NPD4816	Clinical (unspecified phase)
0.57	Remote Similarity	NPD4278	Clinical (unspecified phase)
0.569	Remote Similarity	NPD6946	Approved
0.5673	Remote Similarity	NPD9601	Approved
0.566	Remote Similarity	NPD9603	Phase 3
0.566	Remote Similarity	NPD9602	Phase 3
0.566	Remote Similarity	NPD9604	Approved
0.5648	Remote Similarity	NPD9565	Discontinued
0.5641	Remote Similarity	NPD1428	Phase 2
0.5619	Remote Similarity	NPD9640	Clinical (unspecified phase)
0.5612	Remote Similarity	NPD366	Approved
0.5607	Remote Similarity	NPD867	Phase 3
0.5607	Remote Similarity	NPD868	Phase 3
0.5603	Remote Similarity	NPD6122	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