NPASS Compound

Natural Product: NPC607589

Natural Product ID	NPC607589
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DMXROUYLQHFRCS-GIORXHJXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL402363
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 75 76 0 0 0 0 0 0 0 0999 V2000 -2.6767 -4.9504 0.5606 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5058 -3.7793 0.1017 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9747 -3.9788 0.4427 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9950 -2.5388 0.8188 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6507 -2.1944 0.5404 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.7140 -2.6537 -0.3669 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1344 -3.4839 -1.1560 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7110 -2.2548 -0.4980 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1940 -2.7457 -1.8498 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0636 -0.8627 -0.1588 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5358 -0.5586 -0.5628 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4158 -1.4561 0.1640 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3572 -1.0467 0.9831 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6812 0.3537 1.3022 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5046 0.6220 2.7924 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4106 -0.2165 3.6071 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2820 -0.1981 4.8631 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3949 -1.0214 3.0734 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1936 0.1757 -0.5886 N 0 0 0 0 0 0 0 0 0 0 0 0 0.1385 1.5011 -0.0922 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0741 1.7351 0.6835 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9182 2.5124 -0.4744 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4233 3.3819 -1.6047 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8038 4.1116 -1.1995 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7644 5.3547 -0.6072 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8766 6.0521 -0.2232 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1361 5.4839 -0.4373 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2113 4.2412 -1.0277 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0496 3.5602 -1.4062 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0698 1.7513 -0.7709 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.3994 1.9946 -0.3233 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5493 3.0921 0.0976 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4290 0.8703 -0.4530 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0676 0.9784 -1.8188 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6968 -0.3604 -0.2902 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.9493 -1.4385 0.5741 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0341 -1.4135 1.1098 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7998 -4.6062 1.1765 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3560 -5.5128 1.2856 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3987 -5.6492 -0.2273 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3938 -3.6340 -0.9773 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1434 -3.7200 1.4980 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6069 -3.3484 -0.1888 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1936 -5.0626 0.2980 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0582 -2.8495 1.9151 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2471 -1.4155 1.1407 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2533 -2.9752 0.2427 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3876 -3.3507 -2.3704 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0362 -3.4590 -1.7776 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3769 -1.9121 -2.5626 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1849 -0.7939 0.9870 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7176 0.4837 -0.2962 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6414 -0.6106 -1.6692 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2783 -2.5398 0.0153 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9668 -1.8065 1.4809 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7990 0.4784 1.1315 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1862 1.1231 0.7233 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4328 0.3819 3.0374 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6708 1.6905 2.9978 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2695 -1.1894 3.5347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4501 -0.0206 -1.3397 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0582 3.1721 0.3877 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1090 2.6832 -2.4171 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1909 4.0256 -2.0266 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2081 5.7881 -0.4446 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8636 7.0286 0.2429 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0263 6.0358 -0.1326 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1965 3.8322 -1.1785 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1755 2.6064 -1.8560 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9905 0.9669 -1.4130 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1953 1.0408 0.2916 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7576 0.1143 -1.9273 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3236 1.0431 -2.6369 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7010 1.8841 -1.8836 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8922 -0.5432 -0.8667 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 6 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 10 19 1 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 0 23 24 1 0 24 25 2 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 22 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 33 34 1 0 33 35 1 0 35 36 1 0 36 37 2 0 36 4 1 0 29 24 1 0 1 38 1 0 1 39 1 0 1 40 1 0 2 41 1 0 3 42 1 0 3 43 1 0 3 44 1 0 4 45 1 1 5 46 1 0 8 47 1 1 9 48 1 0 9 49 1 0 9 50 1 0 10 51 1 1 11 52 1 0 11 53 1 0 12 54 1 0 13 55 1 0 14 56 1 0 14 57 1 0 15 58 1 0 15 59 1 0 18 60 1 0 19 61 1 0 22 62 1 1 23 63 1 0 23 64 1 0 25 65 1 0 26 66 1 0 27 67 1 0 28 68 1 0 29 69 1 0 30 70 1 0 33 71 1 1 34 72 1 0 34 73 1 0 34 74 1 0 35 75 1 0 M END

Standard InCHIKey	DMXROUYLQHFRCS-GIORXHJXSA-N
Standard InCHI	InChI=1S/C27H38N4O6/c1-16(2)23-27(37)28-18(4)25(35)30-21(15-19-11-7-5-8-12-19)26(36)29-20(17(3)24(34)31-23)13-9-6-10-14-22(32)33/h5-9,11-12,16-18,20-21,23H,10,13-15H2,1-4H3,(H,28,37)(H,29,36)(H,30,35)(H,31,34)(H,32,33)/b9-6-/t17-,18+,20+,21+,23+/m0/s1
SMILES	CC(C)[C@H]1NC(=O)[C@@H](C)[C@@H](C/C=CCCC(=O)O)NC(=O)[C@@H](Cc2ccccc2)NC(=O)[C@@H](C)NC1=O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088446]
NPO11074	Mycale izuensis	Species	Mycalidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11074	Mycale izuensis	Species	Mycalidae	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	Organism Name	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	11
Ki	7
Inhibition	6
GI	1
EC1000	1
Activity	1

Activity Type	# Activity
Individual protein	22
Cell line	1
Protein complex	1
Protein family	1
Non-molecular	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT689	Individual protein	Histone deacetylase 5	Homo sapiens	Inhibition	<	50.0	%	PMID[23865683]
NPT686	Individual protein	Histone deacetylase 3	Homo sapiens	IC50	=	80.0	nM	PMID[18247554]
NPT689	Individual protein	Histone deacetylase 5	Homo sapiens	IC50	=	10000.0	nM	PMID[18247554]
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	IC50	=	12000.0	nM	PMID[18247554]
NPT5649	Individual protein	Histone deacetylase 10	Homo sapiens	Ki	=	20.0	nM	PMID[23865683]
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	Ki	>	5000.0	nM	PMID[23865683]
NPT691	Individual protein	Histone deacetylase 9	Homo sapiens	Inhibition	<	50.0	%	PMID[23865683]
NPT690	Individual protein	Histone deacetylase 7	Homo sapiens	Inhibition	<	50.0	%	PMID[23865683]
NPT684	Individual protein	Histone deacetylase 1	Homo sapiens	Ki	=	67.0	nM	PMID[23865683]
NPT688	Individual protein	Histone deacetylase 4	Homo sapiens	Inhibition	<	50.0	%	PMID[23865683]
NPT685	Individual protein	Histone deacetylase 2	Homo sapiens	IC50	=	100.0	nM	PMID[18247554]
NPT684	Individual protein	Histone deacetylase 1	Homo sapiens	IC50	=	50.0	nM	PMID[18247554]
NPT692	Individual protein	Histone deacetylase 6	Homo sapiens	IC50	>	50000.0	nM	PMID[18397826]
NPT688	Individual protein	Histone deacetylase 4	Homo sapiens	IC50	=	2280.0	nM	PMID[18397826]
NPT684	Individual protein	Histone deacetylase 1	Homo sapiens	IC50	=	1220.0	nM	PMID[18397826]
NPT690	Individual protein	Histone deacetylase 7	Homo sapiens	IC50	=	9700.0	nM	PMID[18247554]
NPT691	Individual protein	Histone deacetylase 9	Homo sapiens	IC50	=	28000.0	nM	PMID[18247554]
NPT688	Individual protein	Histone deacetylase 4	Homo sapiens	Inhibition	=	30.0	%	PMID[18247554]
NPT685	Individual protein	Histone deacetylase 2	Homo sapiens	Ki	=	50.0	nM	PMID[23865683]
NPT687	Individual protein	Histone deacetylase 8	Homo sapiens	Ki	=	4400.0	nM	PMID[23865683]
NPT5648	Individual protein	Histone deacetylase 11	Homo sapiens	Ki	=	60.0	nM	PMID[23865683]
NPT687	Individual protein	Histone deacetylase 8	Homo sapiens	IC50	=	3700.0	nM	PMID[18247554]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell line	HeLa	Homo sapiens	EC1000	=	17.0	uM	PMID[18397826]
NPT30138	Protein family	Histone deacetylase	Homo sapiens	Inhibition	=	48.0	%	PMID[23291117]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	GI	n.a.	n.a.	n.a.	PMID[25380299]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	n.a.	n.a.	n.a.	PMID[18397826]
NPT29065	Protein complex	Histone deacetylase 3/NCoR1	Homo sapiens	Ki	=	25.0	nM	PMID[23865683]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC607589 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	18544
0.1-0.2	29971
0.2-0.3	1181
0.3-0.4	127
0.4-0.5	25
0.5-0.6	6
0.6-0.7	2
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8333	Intermediate Similarity	NPC601940
0.7692	Intermediate Similarity	NPC602991
0.697	Remote Similarity	NPC601903
0.6389	Remote Similarity	NPC600245
0.5873	Remote Similarity	NPC600079
0.5507	Remote Similarity	NPC606917
0.5333	Remote Similarity	NPC602289
0.5152	Remote Similarity	NPC602452
0.5152	Remote Similarity	NPC607209
0.5079	Remote Similarity	NPC473501

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC607589 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	2697
0.1-0.2	6078
0.2-0.3	367
0.3-0.4	8
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
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
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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