NPASS Compound

Structure

NPC469801 OpenBabel07101718242D 41 43 0 0 1 0 0 0 0 0999 V2000 -12.4789 0.7384 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7474 0.2832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7467 -1.1305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4908 -1.1868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.5979 0.2653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7477 0.7917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8667 0.3186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0165 0.8451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1354 0.3720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8536 2.0046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7346 2.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0033 2.5310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2852 0.8984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5848 1.9513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7683 2.4979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1694 2.7461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5430 1.3967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5327 0.3674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8389 -0.1348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1223 2.0579 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6961 0.8650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2792 2.7803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3014 2.4342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3160 1.8979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0227 0.4430 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4289 0.3674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2588 0.9561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0972 -0.1703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5327 -0.1877 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7211 2.8670 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0713 1.5062 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6173 0.0498 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 -1.6115 3.7235 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1970 2.3710 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2286 0.7121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3111 -1.1472 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2935 1.5198 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4658 2.4244 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1.2991 2.3665 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -0.0519 0.6450 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 2 19 1 0 0 0 0 3 19 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 13 1 0 0 0 0 10 11 1 0 0 0 0 10 12 2 0 0 0 0 11 14 1 0 0 0 0 13 24 1 0 0 0 0 14 39 1 0 0 0 0 15 20 1 0 0 0 0 15 22 1 0 0 0 0 16 23 1 0 0 0 0 16 30 1 0 0 0 0 17 21 2 0 0 0 0 17 40 1 0 0 0 0 18 29 1 0 0 0 0 18 41 1 0 0 0 0 20 12 1 6 0 0 0 20 38 1 0 0 0 0 21 26 1 0 0 0 0 21 31 1 0 0 0 0 22 30 2 3 0 0 0 22 34 1 0 0 0 0 23 31 2 0 0 0 0 23 40 1 0 0 0 0 24 35 2 0 0 0 0 24 39 1 0 0 0 0 25 19 1 1 0 0 0 25 27 1 0 0 0 0 25 32 1 0 0 0 0 26 33 2 0 0 0 0 26 41 1 0 0 0 0 27 36 2 0 0 0 0 27 38 1 0 0 0 0 28 29 1 0 0 0 0 28 32 2 3 0 0 0 28 37 1 0 0 0 0 29 4 1 1 0 0 0 29 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	622.23
Volume:	606.844
LogP:	5.017
LogD:	4.304
LogS:	-4.424
# Rotatable Bonds:	12
TPSA:	126.82
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.194
Synthetic Accessibility Score:	6.665
Fsp3:	0.655
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.926
MDCK Permeability:	1.8942455426440574e-05
Pgp-inhibitor:	0.067
Pgp-substrate:	0.134
Human Intestinal Absorption (HIA):	0.331
20% Bioavailability (F20%):	0.03
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.82
Plasma Protein Binding (PPB):	96.8362808227539%
Volume Distribution (VD):	0.771
Pgp-substrate:	2.1258227825164795%

ADMET: Metabolism

CYP1A2-inhibitor:	0.232
CYP1A2-substrate:	0.716
CYP2C19-inhibitor:	0.91
CYP2C19-substrate:	0.38
CYP2C9-inhibitor:	0.904
CYP2C9-substrate:	0.467
CYP2D6-inhibitor:	0.567
CYP2D6-substrate:	0.124
CYP3A4-inhibitor:	0.961
CYP3A4-substrate:	0.872

ADMET: Excretion

Clearance (CL):	6.811
Half-life (T1/2):	0.315

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.829
Drug-inuced Liver Injury (DILI):	0.947
AMES Toxicity:	0.729
Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.734
Skin Sensitization:	0.101
Carcinogencity:	0.841
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.672

Download Data

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

Natural Product: NPC469801

Natural Product ID:	NPC469801
*Common Name:**	Largazole
IUPAC Name:	n.a.
Synonyms:	Largazole
Standard InCHIKey:	AXESYCSCGBQJBL-SZPBEECKSA-N
Standard InCHI:	InChI=1S/C29H42N4O5S3/c1-5-6-7-8-9-13-24(35)39-14-11-10-12-20-15-22(34)30-16-23-31-21(17-40-23)26-33-29(4,18-41-26)28(37)32-25(19(2)3)27(36)38-20/h10,12,17,19-20,25H,5-9,11,13-16,18H2,1-4H3,(H,30,34)(H,32,37)/b12-10+/t20-,25+,29+/m1/s1
SMILES:	CCCCCCCC(=O)SCC/C=C/[C@H]1OC(=O)[C@@H](N=C(O)[C@]2(C)CSC(=N2)c2nc(CN=C(C1)O)sc2)C(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1173445
PubChem CID:	24757913
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0001961] Depsipeptides [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO11919	Hyrtios reticulatus	Species	Thorectidae	Eukaryota	n.a.	Papua New Guinea	n.a.	PMID[20000782]
NPO11919	Hyrtios reticulatus	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22695182]
NPO40053	Caldora penicillata	Species		Bacteria	n.a.	n.a.	n.a.	PMID[27380142]
NPO40053	Caldora penicillata	Species		Bacteria	n.a.	n.a.	n.a.	PMID[30387355]
NPO11919	Hyrtios reticulatus	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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
EC50	9
GI50	7
IC50	68
Others	50

Activity Type	# Activity
Cell Line	42
Individual Protein	51
NON-MOLECULAR	15
Others	23
Protein Complex	1
Protein Family	1
Tissue	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2678	Cell Line	NB-4	Homo sapiens	Activity	=	5.0	%	PMID[496878]
NPT6328	Individual Protein	Runt-related transcription factor 2	Mus musculus	FC	=	29.0	n.a.	PMID[496879]
NPT2219	Cell Line	C2C12	Mus musculus	FC	=	3.0	n.a.	PMID[496879]
NPT83	Cell Line	MCF7	Homo sapiens	GI	=	5.0	nM	PMID[496880]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	=	10.0	nM	PMID[496881]
NPT5282	Individual Protein	Ubiquitin-like modifier-activating enzyme 1	Homo sapiens	IC50	=	29000.0	nM	PMID[496882]
NPT2652	Individual Protein	SUMO-activating enzyme subunit 1	Homo sapiens	IC50	=	450000.0	nM	PMID[496883]
NPT81	Cell Line	A549	Homo sapiens	Activity	<=	70.0	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	5.3	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	10.6	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	84.1	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	10.8	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	10.4	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	78.8	%	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	3.3	%	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	8.5	%	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	88.2	%	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	3.1	%	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	6.5	%	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	90.4	%	PMID[496886]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	120.0	nM	PMID[496886]
NPT2341	Cell Line	NCI-H1975	Homo sapiens	IC50	=	83.0	nM	PMID[496886]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	77.0	nM	PMID[496886]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	55.0	%	PMID[496890]
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	80.0	%	PMID[496890]
NPT5649	Individual Protein	Histone deacetylase 10	Homo sapiens	IC50	=	2210.0	nM	PMID[496892]
NPT5648	Individual Protein	Histone deacetylase 11	Homo sapiens	IC50	>	10000.0	nM	PMID[496892]
NPT90	Cell Line	DU-145	Homo sapiens	GI50	=	11.0	nM	PMID[496892]
NPT466	Cell Line	U-937	Homo sapiens	GI50	=	16.8	nM	PMID[496892]
NPT6264	Individual Protein	Histone deacetylase 8	Schistosoma mansoni	IC50	>	30000.0	nM	PMID[496896]
NPT6264	Individual Protein	Histone deacetylase 8	Schistosoma mansoni	Inhibition	=	4.0	%	PMID[496896]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	1.6	nM	PMID[496897]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	20.0	nM	PMID[496897]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	460.0	nM	PMID[496898]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	44.0	nM	PMID[496898]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	4750.0	nM	PMID[496898]
NPT146	Cell Line	SK-OV-3	Homo sapiens	IC50	=	250.0	nM	PMID[496898]
NPT1045	Cell Line	U2OS	Homo sapiens	EC50	=	20417.38	nM	PMID[496899]
NPT1045	Cell Line	U2OS	Homo sapiens	EC50	=	371.54	nM	PMID[496899]
NPT1045	Cell Line	U2OS	Homo sapiens	EC50	=	331.13	nM	PMID[496899]
NPT492	Cell Line	Caco-2	Homo sapiens	EC50	<	10000000.0	nM	PMID[496899]
NPT492	Cell Line	Caco-2	Homo sapiens	EC50	=	758.58	nM	PMID[496899]
NPT492	Cell Line	Caco-2	Homo sapiens	EC50	=	14.45	nM	PMID[496899]
NPT744	Cell Line	IMR-32	Homo sapiens	EC50	=	34.67	nM	PMID[496899]
NPT744	Cell Line	IMR-32	Homo sapiens	EC50	=	30.2	nM	PMID[496899]
NPT744	Cell Line	IMR-32	Homo sapiens	EC50	=	12.3	nM	PMID[496899]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	=	65.0	nM	PMID[496900]
NPT517	Cell Line	Panel NCI-60 (60 carcinoma cell lines)	Homo sapiens	GI	=	60.0	%	PMID[496900]
NPT688	Individual Protein	Histone deacetylase 4	Homo sapiens	IC50	=	3000.0	nM	PMID[496878]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	11.4	nM	PMID[496878]
NPT664	Protein Family	Histone deacetylase	Homo sapiens	INH	=	572.0	nM	PMID[496880]
NPT625	Tissue	Liver	Mus musculus	T1/2	<=	0.08333	hr	PMID[496880]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	50.0	%	PMID[496881]
NPT2	Others	Unspecified		IC50	=	29000.0	nM	PMID[496883]
NPT2	Others	Unspecified		Ratio IC50	=	0.02	n.a.	PMID[496884]
NPT691	Individual Protein	Histone deacetylase 9	Homo sapiens	IC50	=	8330.0	nM	PMID[496884]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	604.0	nM	PMID[496884]
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	1720.0	nM	PMID[496884]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	146.0	nM	PMID[496884]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	670.0	nM	PMID[496885]
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	900.0	nM	PMID[496885]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	230.0	nM	PMID[496885]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	340.0	nM	PMID[496885]
NPT27	Others	Unspecified		IC50	>	10000.0	nM	PMID[496886]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	520.0	nM	PMID[496886]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	420.0	nM	PMID[496886]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	140.0	nM	PMID[496886]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	570.0	nM	PMID[496886]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	190.0	nM	PMID[496886]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	13.7	nM	PMID[496887]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	245.0	nM	PMID[496887]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	11500.0	nM	PMID[496887]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	75.0	%	PMID[496888]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	50.0	%	PMID[496888]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	Inhibition	>	90.0	%	PMID[496888]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	Inhibition	=	15.0	%	PMID[496888]
NPT27	Others	Unspecified		Tmax	=	4.0	hr	PMID[496889]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	10.09	nM	PMID[496891]
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	18.65	nM	PMID[496891]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	9.09	nM	PMID[496891]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	165.6	nM	PMID[496891]
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	=	1068.0	nM	PMID[496891]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	24.0	nM	PMID[496891]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	25.0	nM	PMID[496891]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	23.93	nM	PMID[496891]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	24.77	nM	PMID[496891]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	859.0	nM	PMID[496892]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	69.8	nM	PMID[496892]
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	1010.0	nM	PMID[496892]
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	>	10000.0	nM	PMID[496892]
NPT688	Individual Protein	Histone deacetylase 4	Homo sapiens	IC50	>	10000.0	nM	PMID[496892]
NPT689	Individual Protein	Histone deacetylase 5	Homo sapiens	IC50	>	10000.0	nM	PMID[496892]
NPT690	Individual Protein	Histone deacetylase 7	Homo sapiens	IC50	>	10000.0	nM	PMID[496892]
NPT691	Individual Protein	Histone deacetylase 9	Homo sapiens	IC50	>	10000.0	nM	PMID[496892]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	1850.0	nM	PMID[496892]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI50	=	16.2	nM	PMID[496892]
NPT27	Others	Unspecified		GI50	=	39.7	nM	PMID[496892]
NPT27	Others	Unspecified		GI50	=	82.5	nM	PMID[496892]
NPT27	Others	Unspecified		RatioGI50	=	0.28	n.a.	PMID[496892]
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	>	30000.0	nM	PMID[496893]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	9290.0	nM	PMID[496893]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	1360.0	nM	PMID[496893]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	2330.0	nM	PMID[496893]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	6.41	nM	PMID[496894]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	18.0	nM	PMID[496894]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	3.7	nM	PMID[496894]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Emax	=	70.0	%	PMID[496894]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Emax	=	67.0	%	PMID[496894]
NPT2	Others	Unspecified		Ratio IC50	=	0.0	n.a.	PMID[496895]
NPT2	Others	Unspecified		Ratio IC50	=	3.0	n.a.	PMID[496895]
NPT2	Others	Unspecified		Ratio IC50	=	22.0	n.a.	PMID[496895]
NPT2	Others	Unspecified		Ratio IC50	=	7.0	n.a.	PMID[496895]
NPT2	Others	Unspecified		Ratio IC50	=	13.0	n.a.	PMID[496895]
NPT2	Others	Unspecified		Ratio IC50	=	4.0	n.a.	PMID[496895]
NPT2	Others	Unspecified		Ratio IC50	=	2.0	n.a.	PMID[496895]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	228.0	nM	PMID[496898]
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	1520.0	nM	PMID[496898]
NPT4345	Protein Complex	Histone deacetylase 3/Nuclear receptor corepressor 2 (HDAC3/NCoR2)	Homo sapiens	IC50	=	2002.0	nM	PMID[496898]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	>	5000.0	nM	PMID[496898]
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	=	120.0	nM	PMID[496898]
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	61.0	nM	PMID[496900]
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	64.0	nM	PMID[496900]
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	50.0	nM	PMID[496900]
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	1400.0	nM	PMID[496900]
NPT2	Others	Unspecified		Ratio IC50	=	22.0	n.a.	PMID[496900]

☑ 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 NPC469801 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	117
0.1-0.2	1468
0.2-0.3	22654
0.3-0.4	16518
0.4-0.5	1743
0.5-0.6	103
0.6-0.7	58
0.7-0.8	35
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
0.7451	Intermediate Similarity	NPC474069
0.7394	Intermediate Similarity	NPC267605
0.7386	Intermediate Similarity	NPC475390
0.7372	Intermediate Similarity	NPC474080
0.7372	Intermediate Similarity	NPC474102
0.7372	Intermediate Similarity	NPC475683
0.7372	Intermediate Similarity	NPC157194
0.7372	Intermediate Similarity	NPC21449
0.7372	Intermediate Similarity	NPC474079
0.7338	Intermediate Similarity	NPC319751
0.7325	Intermediate Similarity	NPC474067
0.7308	Intermediate Similarity	NPC474064
0.7308	Intermediate Similarity	NPC82436
0.7308	Intermediate Similarity	NPC474103
0.7308	Intermediate Similarity	NPC474068
0.7305	Intermediate Similarity	NPC135558
0.7301	Intermediate Similarity	NPC475554
0.7278	Intermediate Similarity	NPC163147
0.7278	Intermediate Similarity	NPC45576
0.7278	Intermediate Similarity	NPC61667
0.7278	Intermediate Similarity	NPC474090
0.7278	Intermediate Similarity	NPC32583
0.7278	Intermediate Similarity	NPC252616
0.7278	Intermediate Similarity	NPC109498
0.7273	Intermediate Similarity	NPC51692
0.7233	Intermediate Similarity	NPC268063
0.7233	Intermediate Similarity	NPC224609
0.7222	Intermediate Similarity	NPC522
0.7222	Intermediate Similarity	NPC56058
0.7215	Intermediate Similarity	NPC475737
0.7215	Intermediate Similarity	NPC474094
0.7215	Intermediate Similarity	NPC185665
0.7197	Intermediate Similarity	NPC119481
0.7192	Intermediate Similarity	NPC89592
0.7188	Intermediate Similarity	NPC202591
0.717	Intermediate Similarity	NPC206724
0.717	Intermediate Similarity	NPC474515
0.717	Intermediate Similarity	NPC154873
0.7169	Intermediate Similarity	NPC164006
0.7134	Intermediate Similarity	NPC473398
0.7103	Intermediate Similarity	NPC475568
0.7099	Intermediate Similarity	NPC474538
0.7099	Intermediate Similarity	NPC127775
0.7081	Intermediate Similarity	NPC212214
0.7075	Intermediate Similarity	NPC475604
0.7055	Intermediate Similarity	NPC231110
0.7037	Intermediate Similarity	NPC21126
0.7012	Intermediate Similarity	NPC312887
0.7	Intermediate Similarity	NPC74917
0.6994	Remote Similarity	NPC52587
0.6974	Remote Similarity	NPC474070
0.6959	Remote Similarity	NPC132662
0.6954	Remote Similarity	NPC120917
0.6923	Remote Similarity	NPC214375
0.689	Remote Similarity	NPC315252
0.6872	Remote Similarity	NPC165538
0.6835	Remote Similarity	NPC190329
0.6805	Remote Similarity	NPC24990
0.6763	Remote Similarity	NPC476080
0.6763	Remote Similarity	NPC161242
0.6763	Remote Similarity	NPC475534
0.676	Remote Similarity	NPC122427
0.6724	Remote Similarity	NPC475330
0.6686	Remote Similarity	NPC263485
0.6686	Remote Similarity	NPC174652
0.6686	Remote Similarity	NPC25316
0.6686	Remote Similarity	NPC229160
0.6667	Remote Similarity	NPC329961
0.6647	Remote Similarity	NPC216720
0.6608	Remote Similarity	NPC470146
0.6608	Remote Similarity	NPC97078
0.6608	Remote Similarity	NPC101980
0.6607	Remote Similarity	NPC210424
0.659	Remote Similarity	NPC134480
0.6552	Remote Similarity	NPC473704
0.6545	Remote Similarity	NPC14101
0.6474	Remote Similarity	NPC476103
0.645	Remote Similarity	NPC237219
0.6425	Remote Similarity	NPC145178
0.6425	Remote Similarity	NPC14877
0.6425	Remote Similarity	NPC475350
0.6347	Remote Similarity	NPC50274
0.6327	Remote Similarity	NPC251036
0.6311	Remote Similarity	NPC469858
0.6301	Remote Similarity	NPC473886
0.625	Remote Similarity	NPC103268
0.6087	Remote Similarity	NPC96016
0.6066	Remote Similarity	NPC161143
0.6057	Remote Similarity	NPC222391
0.6045	Remote Similarity	NPC34319
0.6045	Remote Similarity	NPC256912
0.6	Remote Similarity	NPC239660
0.6	Remote Similarity	NPC106235
0.5943	Remote Similarity	NPC201014
0.5943	Remote Similarity	NPC110129
0.5896	Remote Similarity	NPC475196
0.5808	Remote Similarity	NPC478251
0.5808	Remote Similarity	NPC478252
0.5806	Remote Similarity	NPC278902
0.5782	Remote Similarity	NPC329305
0.5771	Remote Similarity	NPC217981
0.5731	Remote Similarity	NPC283783
0.5724	Remote Similarity	NPC201968
0.5687	Remote Similarity	NPC275393

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 NPC469801 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	92
0.1-0.2	423
0.2-0.3	3170
0.3-0.4	4620
0.4-0.5	771
0.5-0.6	65
0.6-0.7	8
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
0.7215	Intermediate Similarity	NPD6907	Phase 2
0.7212	Intermediate Similarity	NPD6916	Clinical (unspecified phase)
0.7037	Intermediate Similarity	NPD6910	Phase 3
0.6933	Remote Similarity	NPD6911	Discontinued
0.6871	Remote Similarity	NPD6915	Approved
0.6441	Remote Similarity	NPD2957	Phase 2
0.6241	Remote Similarity	NPD6094	Approved
0.6241	Remote Similarity	NPD6095	Approved
0.6	Remote Similarity	NPD8339	Clinical (unspecified phase)
0.5978	Remote Similarity	NPD6270	Approved
0.589	Remote Similarity	NPD6413	Approved
0.5889	Remote Similarity	NPD3332	Approved
0.5889	Remote Similarity	NPD3333	Approved
0.5879	Remote Similarity	NPD3876	Approved
0.5851	Remote Similarity	NPD6632	Clinical (unspecified phase)
0.5824	Remote Similarity	NPD3877	Approved
0.5806	Remote Similarity	NPD9579	Approved
0.5802	Remote Similarity	NPD1083	Clinical (unspecified phase)
0.5747	Remote Similarity	NPD5189	Clinical (unspecified phase)
0.573	Remote Similarity	NPD3966	Clinical (unspecified phase)
0.5707	Remote Similarity	NPD6348	Clinical (unspecified phase)
0.5682	Remote Similarity	NPD5634	Approved
0.5638	Remote Similarity	NPD7977	Clinical (unspecified phase)

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