NPASS Compound

Structure

CID313272 OpenBabel06191716122D 23 24 0 0 1 0 0 0 0 0999 V2000 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 5 2 0 0 0 0 1 7 1 0 0 0 0 2 6 1 0 0 0 0 2 8 1 0 0 0 0 3 5 1 0 0 0 0 3 16 1 0 0 0 0 4 6 1 0 0 0 0 4 17 1 0 0 0 0 5 9 1 0 0 0 0 6 10 1 0 0 0 0 7 11 1 0 0 0 0 7 15 1 0 0 0 0 8 12 1 0 0 0 0 8 15 1 0 0 0 0 9 13 1 0 0 0 0 9 18 1 0 0 0 0 10 14 1 0 0 0 0 10 19 1 0 0 0 0 11 13 1 0 0 0 0 11 20 1 0 0 0 0 12 14 1 0 0 0 0 12 21 1 0 0 0 0 13 22 1 0 0 0 0 14 23 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

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

Natural Product: NPC313272

*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
GI50	45

Activity Type	# Activity
Cell Line	45

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT368	Cell Line	SN12C	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT370	Cell Line	NCI-H23	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT371	Cell Line	UO-31	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT369	Cell Line	ACHN	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT374	Cell Line	SF-539	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT375	Cell Line	Malme-3M	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT111	Cell Line	K562	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT377	Cell Line	OVCAR-3	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT379	Cell Line	HOP-62	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT112	Cell Line	MOLT-4	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT380	Cell Line	U-251	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT381	Cell Line	OVCAR-8	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT383	Cell Line	SNB-19	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT572	Cell Line	DMS-273	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT573	Cell Line	M19-MEL	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT323	Cell Line	SW-620	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT384	Cell Line	TK-10	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT455	Cell Line	NCI-H522	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT387	Cell Line	M14	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT386	Cell Line	KM12	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT574	Cell Line	XF498	Homo sapiens	GI50	n.a.	64863.44	nM	PMID[510237]
NPT388	Cell Line	NCI-H322M	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT389	Cell Line	RPMI-8226	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT390	Cell Line	LOX IMVI	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT81	Cell Line	A549	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT392	Cell Line	SNB-75	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT148	Cell Line	HCT-15	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT394	Cell Line	EKVX	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT576	Cell Line	DMS-114	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT146	Cell Line	SK-OV-3	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT398	Cell Line	UACC-62	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT399	Cell Line	SF-295	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT458	Cell Line	IGROV-1	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT401	Cell Line	786-0	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT403	Cell Line	UACC-257	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT579	Cell Line	DLD-1	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT405	Cell Line	NCI-H226	Homo sapiens	GI50	n.a.	94406.09	nM	PMID[510237]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT139	Cell Line	HT-29	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT406	Cell Line	RXF 393	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT407	Cell Line	COLO 205	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]
NPT732	Cell Line	HOP-18	Homo sapiens	GI50	n.a.	100000.0	nM	PMID[510237]

☑ 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 NPC313272 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	120
0.1-0.2	835
0.2-0.3	6564
0.3-0.4	24895
0.4-0.5	9385
0.5-0.6	863
0.6-0.7	29
0.7-0.8	2
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC319537
0.875	High Similarity	NPC20035
0.835	Intermediate Similarity	NPC315170
0.7449	Intermediate Similarity	NPC314762
0.7041	Intermediate Similarity	NPC244539
0.7034	Intermediate Similarity	NPC314306
0.68	Remote Similarity	NPC478138
0.68	Remote Similarity	NPC313762
0.6557	Remote Similarity	NPC241597
0.6218	Remote Similarity	NPC473254
0.6204	Remote Similarity	NPC297058
0.619	Remote Similarity	NPC304646
0.619	Remote Similarity	NPC28280
0.6182	Remote Similarity	NPC470365
0.6136	Remote Similarity	NPC237286
0.6119	Remote Similarity	NPC471471
0.6119	Remote Similarity	NPC121601
0.6119	Remote Similarity	NPC164476
0.6048	Remote Similarity	NPC472359
0.6034	Remote Similarity	NPC25033
0.6034	Remote Similarity	NPC476261
0.6034	Remote Similarity	NPC119225
0.6034	Remote Similarity	NPC470382
0.6034	Remote Similarity	NPC471635
0.6	Remote Similarity	NPC176012
0.595	Remote Similarity	NPC55336
0.594	Remote Similarity	NPC296686
0.5935	Remote Similarity	NPC315426
0.5932	Remote Similarity	NPC140300
0.5932	Remote Similarity	NPC474164
0.5931	Remote Similarity	NPC233770
0.5931	Remote Similarity	NPC77481
0.5929	Remote Similarity	NPC316186
0.5926	Remote Similarity	NPC207657
0.5902	Remote Similarity	NPC477000
0.5902	Remote Similarity	NPC477001
0.5887	Remote Similarity	NPC159367
0.5872	Remote Similarity	NPC471270
0.5854	Remote Similarity	NPC93179
0.5842	Remote Similarity	NPC471418
0.5839	Remote Similarity	NPC478139
0.5833	Remote Similarity	NPC56298
0.5833	Remote Similarity	NPC471628
0.5806	Remote Similarity	NPC46981
0.5797	Remote Similarity	NPC15249
0.5797	Remote Similarity	NPC25455
0.5794	Remote Similarity	NPC287764
0.5789	Remote Similarity	NPC469943
0.5784	Remote Similarity	NPC268922
0.578	Remote Similarity	NPC236707
0.578	Remote Similarity	NPC95124
0.578	Remote Similarity	NPC471266
0.5772	Remote Similarity	NPC44514
0.5769	Remote Similarity	NPC474468
0.5755	Remote Similarity	NPC122819
0.5745	Remote Similarity	NPC208757
0.5741	Remote Similarity	NPC68119
0.5741	Remote Similarity	NPC13823
0.5739	Remote Similarity	NPC259875
0.5739	Remote Similarity	NPC187785
0.5739	Remote Similarity	NPC473100
0.5738	Remote Similarity	NPC247060
0.5738	Remote Similarity	NPC50815
0.5735	Remote Similarity	NPC96010
0.5735	Remote Similarity	NPC317654
0.5728	Remote Similarity	NPC473710
0.5728	Remote Similarity	NPC475694
0.5726	Remote Similarity	NPC55462
0.5725	Remote Similarity	NPC322366
0.5714	Remote Similarity	NPC85001
0.5714	Remote Similarity	NPC253645
0.5714	Remote Similarity	NPC147753
0.5714	Remote Similarity	NPC26932
0.5714	Remote Similarity	NPC150057
0.5714	Remote Similarity	NPC289140
0.5714	Remote Similarity	NPC476903
0.5714	Remote Similarity	NPC95920
0.5714	Remote Similarity	NPC147835
0.5714	Remote Similarity	NPC242692
0.5704	Remote Similarity	NPC68327
0.5703	Remote Similarity	NPC76660
0.5703	Remote Similarity	NPC276995
0.57	Remote Similarity	NPC142290
0.57	Remote Similarity	NPC471892
0.57	Remote Similarity	NPC471780
0.57	Remote Similarity	NPC198341
0.57	Remote Similarity	NPC75435
0.57	Remote Similarity	NPC223386
0.569	Remote Similarity	NPC84171
0.569	Remote Similarity	NPC473099
0.5673	Remote Similarity	NPC476695
0.5673	Remote Similarity	NPC285014
0.5673	Remote Similarity	NPC28959
0.5673	Remote Similarity	NPC299603
0.5673	Remote Similarity	NPC255535
0.5673	Remote Similarity	NPC476694
0.5673	Remote Similarity	NPC137554
0.5673	Remote Similarity	NPC476696
0.5672	Remote Similarity	NPC472458
0.5659	Remote Similarity	NPC478137
0.5656	Remote Similarity	NPC118275
0.5644	Remote Similarity	NPC116377
0.5644	Remote Similarity	NPC315980
0.5644	Remote Similarity	NPC69798
0.5644	Remote Similarity	NPC303798
0.5644	Remote Similarity	NPC473952
0.5644	Remote Similarity	NPC101746
0.5644	Remote Similarity	NPC77191
0.5644	Remote Similarity	NPC286851
0.5641	Remote Similarity	NPC97404
0.5641	Remote Similarity	NPC41554
0.5641	Remote Similarity	NPC160931
0.5641	Remote Similarity	NPC37205
0.5625	Remote Similarity	NPC29501
0.562	Remote Similarity	NPC476951
0.5615	Remote Similarity	NPC476499
0.5614	Remote Similarity	NPC255143
0.5612	Remote Similarity	NPC323775
0.5612	Remote Similarity	NPC236347
0.561	Remote Similarity	NPC471083
0.561	Remote Similarity	NPC251884
0.5607	Remote Similarity	NPC140327
0.5607	Remote Similarity	NPC212008
0.5607	Remote Similarity	NPC51055
0.5607	Remote Similarity	NPC62293
0.5606	Remote Similarity	NPC235625
0.5603	Remote Similarity	NPC470361
0.5603	Remote Similarity	NPC120420
0.56	Remote Similarity	NPC475837
0.56	Remote Similarity	NPC471259

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 NPC313272 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	91
0.1-0.2	472
0.2-0.3	3411
0.3-0.4	3907
0.4-0.5	1125
0.5-0.6	136
0.6-0.7	7
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.77	Intermediate Similarity	NPD394	Phase 3
0.7034	Intermediate Similarity	NPD6430	Approved
0.7034	Intermediate Similarity	NPD6429	Approved
0.6721	Remote Similarity	NPD4831	Approved
0.6721	Remote Similarity	NPD4832	Approved
0.6721	Remote Similarity	NPD4830	Approved
0.6557	Remote Similarity	NPD3731	Phase 3
0.6406	Remote Similarity	NPD6436	Phase 3
0.5971	Remote Similarity	NPD1136	Approved
0.5971	Remote Similarity	NPD1130	Approved
0.5971	Remote Similarity	NPD1132	Approved
0.5957	Remote Similarity	NPD817	Approved
0.5957	Remote Similarity	NPD823	Approved
0.5899	Remote Similarity	NPD597	Approved
0.5899	Remote Similarity	NPD598	Approved
0.5899	Remote Similarity	NPD601	Approved
0.5845	Remote Similarity	NPD2568	Approved
0.5839	Remote Similarity	NPD602	Approved
0.5839	Remote Similarity	NPD599	Approved
0.5833	Remote Similarity	NPD4837	Approved
0.5833	Remote Similarity	NPD4838	Approved
0.5833	Remote Similarity	NPD4836	Approved
0.5833	Remote Similarity	NPD4835	Approved
0.5816	Remote Similarity	NPD3061	Approved
0.5816	Remote Similarity	NPD3062	Approved
0.5816	Remote Similarity	NPD3059	Approved
0.5755	Remote Similarity	NPD8449	Approved
0.5738	Remote Similarity	NPD244	Clinical (unspecified phase)
0.5734	Remote Similarity	NPD5314	Approved
0.5726	Remote Similarity	NPD5357	Phase 1
0.5725	Remote Similarity	NPD859	Approved
0.5725	Remote Similarity	NPD858	Approved
0.5714	Remote Similarity	NPD8450	Suspended
0.5667	Remote Similarity	NPD4282	Approved
0.5634	Remote Similarity	NPD8387	Clinical (unspecified phase)
0.5612	Remote Similarity	NPD9619	Approved
0.5612	Remote Similarity	NPD9620	Approved
0.5612	Remote Similarity	NPD9621	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