NPASS Natural Product

Natural Product: NPC469801

Natural Product ID:	NPC469801
Common Name:	Largazole
IUPAC Name:
Synonyms:	Largazole
Molecular Formula:	C29H42N4O5S3
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
Canonical 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
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO11919	Hyrtios reticulatus	Species	Thorectidae	Eukaryota				PMID[22695182]

Biological Activity

Activity Type	# Activity
GI50	6
IC50	49
Others	26

Activity Type	# Activity
Cell Line	25
Individual Protein	41
Others	15

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT90	Cell Line	DU-145	Homo sapiens	GI50	=	11	nM	PubChem BioAssay data set
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	50	%	22365754
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	75	%	22365754
NPT2	Others	Unspecified		GI50	=	82.5	nM	16408017
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	340	nM	12828469
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	9290	nM	11520225
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	13.7	nM	21334794
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	=	10	nM	20146479
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	11.4	nM	20655237
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	10.09	nM	23102654
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	1720	nM	16933872
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	146	nM	16933872
NPT2	Others	Unspecified		IC50	=	29000	nM	Open TG-GATES in vivo data: Biochemistry
NPT2652	Individual Protein	SUMO-activating enzyme subunit 1	Homo sapiens	IC50	=	450000	nM	Open TG-GATES in vivo data: Biochemistry
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	Inhibition	>	90	%	Open TG-GATES in vivo data: Hematology
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	Inhibition	=	15	%	Open TG-GATES in vivo data: Hematology
NPT690	Individual Protein	Histone deacetylase 7	Homo sapiens	IC50	>	10000	nM	10.1007/s00044-011-9879-7
NPT691	Individual Protein	Histone deacetylase 9	Homo sapiens	IC50	>	10000	nM	10.1007/s00044-011-9879-7
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	1360	nM	24164245
NPT81	Cell Line	A549	Homo sapiens	Activity	<=	70	%	26349626
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	10.4	%	26349626
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	10.8	%	26349626
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	84.1	%	26349626
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	900	nM	22705020
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	11500	nM	20346682
NPT83	Cell Line	MCF7	Homo sapiens	GI	=	5	nM	24164206
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	>	10000	nM	22530779
NPT2	Others	Unspecified		Ratio IC50	=	0.02		10.6019/CHEMBL1201861
NPT5648	Individual Protein	Histone deacetylase 11	Homo sapiens	IC50	>	10000	nM	10096871
NPT2	Others	Unspecified		IC50	=	23.93	nM	16309317
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	>	30000	nM	20159656
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	670	nM	19459645
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	230	nM	10998351
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	1850	nM	23398362
NPT688	Individual Protein	Histone deacetylase 4	Homo sapiens	IC50	>	10000	nM	10757713
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	5.3	%	15620248
NPT81	Cell Line	A549	Homo sapiens	Activity	=	3.3	%	19733087
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	78.8	%	20541427
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	1010	nM	23507152
NPT691	Individual Protein	Histone deacetylase 9	Homo sapiens	IC50	=	8330	nM	22901896
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	55	%	25819096
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	9.09	nM	19114678
NPT397	Cell Line	NCI-H460	Homo sapiens	Activity	=	10.6	%	19596885
NPT2	Others	Unspecified		IC50	=	24.77	nM	10.6019/CHEMBL1201861
NPT5649	Individual Protein	Histone deacetylase 10	Homo sapiens	IC50	=	2210	nM	20429578
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	120	nM	18070958
NPT2	Others	Unspecified		IC50	=	190	nM	18070958
NPT2	Others	Unspecified		IC50	=	520	nM	19827833
NPT2	Others	Unspecified		IC50	=	140	nM	20070106
NPT466	Cell Line	U-937	Homo sapiens	GI50	=	16.8	nM	19555122
NPT2	Others	Unspecified		GI50	=	16.2	nM	22148349
NPT139	Cell Line	HT-29	Homo sapiens	Activity	=	80	%	25211145
NPT2219	Cell Line	C2C12	Mus musculus	FC	=	3		11908979
NPT689	Individual Protein	Histone deacetylase 5	Homo sapiens	IC50	>	10000	nM	13678412
NPT685	Individual Protein	Histone deacetylase 2	Homo sapiens	IC50	=	18.65	nM	12361396
NPT2	Others	Unspecified		IC50	=	24	nM	16378375
NPT81	Cell Line	A549	Homo sapiens	IC50	=	77	nM	7561908
NPT2341	Cell Line	NCI-H1975	Homo sapiens	IC50	=	83	nM	16124770
NPT2	Others	Unspecified		IC50	=	420	nM	16124770
NPT2	Others	Unspecified		IC50	=	570	nM	17336534
NPT2678	Cell Line	NB-4	Homo sapiens	Activity	=	5	%	12467636
NPT5282	Individual Protein	Ubiquitin-like modifier-activating enzyme 1	Homo sapiens	IC50	=	29000	nM	3204377
NPT2	Others	Unspecified		IC50	>	10000	nM	20045651
NPT81	Cell Line	A549	Homo sapiens	Activity	=	3.1	%	20045651
NPT81	Cell Line	A549	Homo sapiens	Activity	=	6.5	%	20045651
NPT81	Cell Line	A549	Homo sapiens	Activity	=	8.5	%	20045651
NPT81	Cell Line	A549	Homo sapiens	Activity	=	88.2	%	26083682
NPT81	Cell Line	A549	Homo sapiens	Activity	=	90.4	%	26083682
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	859	nM	23031087
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	Inhibition	=	50	%	22449077
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	2330	nM	23145909
NPT2	Others	Unspecified		GI50	=	39.7	nM	16499321
NPT6328	Individual Protein	Runt-related transcription factor 2	Mus musculus	FC	=	29		17194835
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	245	nM	18625769
NPT688	Individual Protein	Histone deacetylase 4	Homo sapiens	IC50	=	3000	nM	20805391
NPT684	Individual Protein	Histone deacetylase 1	Homo sapiens	IC50	=	69.8	nM	8946741
NPT687	Individual Protein	Histone deacetylase 8	Homo sapiens	IC50	=	1068	nM	26046820
NPT692	Individual Protein	Histone deacetylase 6	Homo sapiens	IC50	=	165.6	nM	25735399
NPT686	Individual Protein	Histone deacetylase 3	Homo sapiens	IC50	=	604	nM	24079882
NPT2	Others	Unspecified		IC50	=	25	nM	18829331
NPT2678	Cell Line	NB-4	Homo sapiens	Activity	=	5	%	17503850

Similar Natural Products 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	85
0.1-0.2	902
0.2-0.3	14980
0.3-0.4	13069
0.4-0.5	1687
0.5-0.6	73
0.6-0.7	44
0.7-0.8	49
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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

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	87
0.1-0.2	381
0.2-0.3	2469
0.3-0.4	5000
0.4-0.5	1151
0.5-0.6	64
0.6-0.7	6
0.7-0.8	3
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)

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 $$$$

External Identifiers

PubChem CID	24757913
ChEMBL	CHEMBL1173445
ZINC

Physicochemical Properties

Molecular Weight:	622.23
ALogP:	0.62
MLogP:	3.33
XLogP:	5.674
# Rotatable Bonds:	18
Polar Surface Area:	212.64
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	41

Download Data

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