NPASS Compound

Structure

CID314523 OpenBabel06191716122D 38 40 0 0 1 0 0 0 0 0999 V2000 -0.3520 -2.4496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9663 -1.3262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6420 2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0889 -2.1930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4784 0.7406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1078 2.5195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7041 1.7148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5961 1.6603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4646 -1.5767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4644 -1.5995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9982 -0.1366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4489 3.2717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3452 3.6634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0261 5.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1309 5.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2794 4.1201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0172 -1.5073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6586 2.7138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5081 -1.2851 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -5.7873 4.4933 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -4.1182 5.5611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4215 4.6155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6209 1.8816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4332 -1.3517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1374 5.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6657 -0.7462 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.1737 3.8118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4397 0.8981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2992 -0.8517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.2113 5.2287 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.5299 2.8774 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.5335 5.1590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4099 6.5176 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8106 -2.2777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0509 4.2920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3894 0.5848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1374 4.6155 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 4 19 1 0 0 0 0 5 7 2 0 0 0 0 5 11 1 0 0 0 0 6 8 1 0 0 0 0 6 12 1 0 0 0 0 7 18 1 0 0 0 0 8 23 2 0 0 0 0 9 10 2 0 0 0 0 9 19 1 0 0 0 0 10 24 1 0 0 0 0 11 29 1 0 0 0 0 12 31 1 0 0 0 0 13 18 2 0 0 0 0 13 20 1 0 0 0 0 14 20 1 0 0 0 0 14 21 1 0 0 0 0 15 21 1 0 0 0 0 15 25 1 0 0 0 0 16 22 2 0 0 0 0 16 37 1 0 0 0 0 17 26 1 0 0 0 0 19 26 1 0 0 0 0 20 32 1 0 0 0 0 21 33 2 0 0 0 0 22 27 1 0 0 0 0 22 30 1 0 0 0 0 23 28 1 0 0 0 0 23 31 1 0 0 0 0 24 29 2 3 0 0 0 24 34 1 0 0 0 0 25 30 2 0 0 0 0 25 37 1 0 0 0 0 26 38 1 0 0 0 0 27 31 1 0 0 0 0 27 35 2 0 0 0 0 28 36 2 0 0 0 0 28 38 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: NPC314523

*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	56

Activity Type	# Activity
Cell Line	56

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT368	Cell Line	SN12C	Homo sapiens	GI50	n.a.	14893.61	nM	PMID[521212]
NPT367	Cell Line	MDA-N	Homo sapiens	GI50	n.a.	14190.58	nM	PMID[521212]
NPT370	Cell Line	NCI-H23	Homo sapiens	GI50	n.a.	17100.15	nM	PMID[521212]
NPT369	Cell Line	ACHN	Homo sapiens	GI50	n.a.	12502.59	nM	PMID[521212]
NPT116	Cell Line	HL-60	Homo sapiens	GI50	n.a.	20323.57	nM	PMID[521212]
NPT90	Cell Line	DU-145	Homo sapiens	GI50	n.a.	27101.92	nM	PMID[521212]
NPT374	Cell Line	SF-539	Homo sapiens	GI50	n.a.	30060.76	nM	PMID[521212]
NPT375	Cell Line	Malme-3M	Homo sapiens	GI50	n.a.	11694.99	nM	PMID[521212]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	GI50	n.a.	33419.5	nM	PMID[521212]
NPT111	Cell Line	K562	Homo sapiens	GI50	n.a.	30974.19	nM	PMID[521212]
NPT376	Cell Line	A498	Homo sapiens	GI50	n.a.	23604.78	nM	PMID[521212]
NPT377	Cell Line	OVCAR-3	Homo sapiens	GI50	n.a.	19815.27	nM	PMID[521212]
NPT379	Cell Line	HOP-62	Homo sapiens	GI50	n.a.	31477.48	nM	PMID[521212]
NPT112	Cell Line	MOLT-4	Homo sapiens	GI50	n.a.	16557.7	nM	PMID[521212]
NPT380	Cell Line	U-251	Homo sapiens	GI50	n.a.	35809.64	nM	PMID[521212]
NPT381	Cell Line	OVCAR-8	Homo sapiens	GI50	n.a.	15275.66	nM	PMID[521212]
NPT382	Cell Line	OVCAR-5	Homo sapiens	GI50	n.a.	18836.49	nM	PMID[521212]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	GI50	n.a.	23878.11	nM	PMID[521212]
NPT383	Cell Line	SNB-19	Homo sapiens	GI50	n.a.	89330.55	nM	PMID[521212]
NPT384	Cell Line	TK-10	Homo sapiens	GI50	n.a.	31550.05	nM	PMID[521212]
NPT385	Cell Line	SR	Homo sapiens	GI50	n.a.	15031.42	nM	PMID[521212]
NPT323	Cell Line	SW-620	Homo sapiens	GI50	n.a.	18113.4	nM	PMID[521212]
NPT386	Cell Line	KM12	Homo sapiens	GI50	n.a.	12416.52	nM	PMID[521212]
NPT455	Cell Line	NCI-H522	Homo sapiens	GI50	n.a.	176.2	nM	PMID[521212]
NPT387	Cell Line	M14	Homo sapiens	GI50	n.a.	17338.04	nM	PMID[521212]
NPT389	Cell Line	RPMI-8226	Homo sapiens	GI50	n.a.	12882.5	nM	PMID[521212]
NPT388	Cell Line	NCI-H322M	Homo sapiens	GI50	n.a.	28183.83	nM	PMID[521212]
NPT456	Cell Line	OVCAR-4	Homo sapiens	GI50	n.a.	57942.87	nM	PMID[521212]
NPT390	Cell Line	LOX IMVI	Homo sapiens	GI50	n.a.	17179.08	nM	PMID[521212]
NPT457	Cell Line	BT-549	Homo sapiens	GI50	n.a.	20511.62	nM	PMID[521212]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	GI50	n.a.	17418.07	nM	PMID[521212]
NPT81	Cell Line	A549	Homo sapiens	GI50	n.a.	29922.65	nM	PMID[521212]
NPT392	Cell Line	SNB-75	Homo sapiens	GI50	n.a.	11297.96	nM	PMID[521212]
NPT391	Cell Line	HCC 2998	Homo sapiens	GI50	n.a.	19098.53	nM	PMID[521212]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	n.a.	14487.72	nM	PMID[521212]
NPT148	Cell Line	HCT-15	Homo sapiens	GI50	n.a.	19769.7	nM	PMID[521212]
NPT395	Cell Line	SF-268	Homo sapiens	GI50	n.a.	16032.45	nM	PMID[521212]
NPT83	Cell Line	MCF7	Homo sapiens	GI50	n.a.	19142.56	nM	PMID[521212]
NPT394	Cell Line	EKVX	Homo sapiens	GI50	n.a.	18793.17	nM	PMID[521212]
NPT306	Cell Line	PC-3	Homo sapiens	GI50	n.a.	27101.92	nM	PMID[521212]
NPT146	Cell Line	SK-OV-3	Homo sapiens	GI50	n.a.	53088.44	nM	PMID[521212]
NPT396	Cell Line	T47D	Homo sapiens	GI50	n.a.	12189.9	nM	PMID[521212]
NPT398	Cell Line	UACC-62	Homo sapiens	GI50	n.a.	15995.58	nM	PMID[521212]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI50	n.a.	53951.06	nM	PMID[521212]
NPT308	Cell Line	CAKI-1	Homo sapiens	GI50	n.a.	21978.6	nM	PMID[521212]
NPT400	Cell Line	MDA-MB-435	Homo sapiens	GI50	n.a.	24831.33	nM	PMID[521212]
NPT399	Cell Line	SF-295	Homo sapiens	GI50	n.a.	47973.34	nM	PMID[521212]
NPT458	Cell Line	IGROV-1	Homo sapiens	GI50	n.a.	16595.87	nM	PMID[521212]
NPT402	Cell Line	Hs-578T	Homo sapiens	GI50	n.a.	19998.62	nM	PMID[521212]
NPT403	Cell Line	UACC-257	Homo sapiens	GI50	n.a.	35318.32	nM	PMID[521212]
NPT401	Cell Line	786-0	Homo sapiens	GI50	n.a.	20844.91	nM	PMID[521212]
NPT404	Cell Line	CCRF-CEM	Homo sapiens	GI50	n.a.	21577.44	nM	PMID[521212]
NPT405	Cell Line	NCI-H226	Homo sapiens	GI50	n.a.	17660.38	nM	PMID[521212]
NPT139	Cell Line	HT-29	Homo sapiens	GI50	n.a.	15488.17	nM	PMID[521212]
NPT170	Cell Line	SK-MEL-28	Homo sapiens	GI50	n.a.	19588.45	nM	PMID[521212]
NPT407	Cell Line	COLO 205	Homo sapiens	GI50	n.a.	16330.52	nM	PMID[521212]

☑ 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 NPC314523 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	207
0.1-0.2	1789
0.2-0.3	9802
0.3-0.4	24192
0.4-0.5	6055
0.5-0.6	586
0.6-0.7	28
0.7-0.8	32
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC58001
0.7656	Intermediate Similarity	NPC476829
0.764	Intermediate Similarity	NPC30527
0.7458	Intermediate Similarity	NPC211555
0.7452	Intermediate Similarity	NPC325683
0.744	Intermediate Similarity	NPC477219
0.7404	Intermediate Similarity	NPC37924
0.7401	Intermediate Similarity	NPC186452
0.7368	Intermediate Similarity	NPC476828
0.7311	Intermediate Similarity	NPC322800
0.7311	Intermediate Similarity	NPC477218
0.7311	Intermediate Similarity	NPC168135
0.7273	Intermediate Similarity	NPC476830
0.7264	Intermediate Similarity	NPC177432
0.7264	Intermediate Similarity	NPC299035
0.7238	Intermediate Similarity	NPC12660
0.7225	Intermediate Similarity	NPC476826
0.7225	Intermediate Similarity	NPC476827
0.7225	Intermediate Similarity	NPC476831
0.7204	Intermediate Similarity	NPC476832
0.7198	Intermediate Similarity	NPC54983
0.6866	Remote Similarity	NPC224395
0.6866	Remote Similarity	NPC208297
0.6816	Remote Similarity	NPC107458
0.6816	Remote Similarity	NPC295653
0.6748	Remote Similarity	NPC258022
0.67	Remote Similarity	NPC58112
0.67	Remote Similarity	NPC88938
0.67	Remote Similarity	NPC306300
0.665	Remote Similarity	NPC103452
0.665	Remote Similarity	NPC199461
0.665	Remote Similarity	NPC46313
0.6585	Remote Similarity	NPC289029
0.6585	Remote Similarity	NPC48323
0.6512	Remote Similarity	NPC309919
0.6504	Remote Similarity	NPC477586
0.6504	Remote Similarity	NPC477590
0.6504	Remote Similarity	NPC477588
0.6504	Remote Similarity	NPC477585
0.6443	Remote Similarity	NPC475455
0.6416	Remote Similarity	NPC477587
0.6416	Remote Similarity	NPC477589
0.621	Remote Similarity	NPC49195
0.6023	Remote Similarity	NPC120335
0.5876	Remote Similarity	NPC237219
0.5781	Remote Similarity	NPC50274
0.5753	Remote Similarity	NPC316403
0.5739	Remote Similarity	NPC309525
0.5721	Remote Similarity	NPC220408
0.5676	Remote Similarity	NPC314222
0.5676	Remote Similarity	NPC196449
0.5645	Remote Similarity	NPC472436
0.5636	Remote Similarity	NPC472287
0.5636	Remote Similarity	NPC472286
0.5625	Remote Similarity	NPC119481
0.5619	Remote Similarity	NPC475342
0.5617	Remote Similarity	NPC475196
0.5615	Remote Similarity	NPC165964
0.5614	Remote Similarity	NPC313804
0.5614	Remote Similarity	NPC315804
0.5607	Remote Similarity	NPC59827
0.5607	Remote Similarity	NPC184933
0.5605	Remote Similarity	NPC476514
0.5602	Remote Similarity	NPC316224

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 NPC314523 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	138
0.1-0.2	494
0.2-0.3	1885
0.3-0.4	4037
0.4-0.5	2419
0.5-0.6	170
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8626	High Similarity	NPD7896	Approved
0.6502	Remote Similarity	NPD6347	Phase 2
0.639	Remote Similarity	NPD7490	Discontinued
0.625	Remote Similarity	NPD6857	Phase 3
0.6227	Remote Similarity	NPD7180	Phase 3
0.6109	Remote Similarity	NPD6974	Phase 3
0.6096	Remote Similarity	NPD7031	Phase 1
0.6	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.5973	Remote Similarity	NPD2433	Clinical (unspecified phase)
0.5939	Remote Similarity	NPD4898	Clinical (unspecified phase)
0.588	Remote Similarity	NPD7853	Phase 2
0.5856	Remote Similarity	NPD4667	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD7284	Clinical (unspecified phase)
0.5823	Remote Similarity	NPD7022	Phase 2
0.5813	Remote Similarity	NPD2957	Phase 2
0.5808	Remote Similarity	NPD3263	Phase 3
0.5804	Remote Similarity	NPD5443	Clinical (unspecified phase)
0.5801	Remote Similarity	NPD1659	Phase 1
0.5787	Remote Similarity	NPD4368	Phase 2
0.5785	Remote Similarity	NPD1638	Discovery
0.5763	Remote Similarity	NPD4394	Clinical (unspecified phase)
0.5748	Remote Similarity	NPD772	Phase 3
0.5739	Remote Similarity	NPD5640	Discontinued
0.5721	Remote Similarity	NPD7811	Phase 3
0.5721	Remote Similarity	NPD7810	Phase 3
0.5714	Remote Similarity	NPD2779	Approved
0.5696	Remote Similarity	NPD6247	Clinical (unspecified phase)
0.567	Remote Similarity	NPD3945	Discontinued
0.5669	Remote Similarity	NPD5922	Phase 3
0.5636	Remote Similarity	NPD2951	Discontinued
0.5625	Remote Similarity	NPD5866	Approved
0.5622	Remote Similarity	NPD8104	Phase 3
0.5605	Remote Similarity	NPD3392	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