NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	574.5
Volume:	670.487
LogP:	8.937
LogD:	4.505
LogS:	-2.389
# Rotatable Bonds:	32
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.049
Synthetic Accessibility Score:	2.974
Fsp3:	0.757
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.145
MDCK Permeability:	2.4320981538039632e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.151
30% Bioavailability (F30%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	96.98870849609375%
Volume Distribution (VD):	0.862
Pgp-substrate:	0.8635015487670898%

ADMET: Metabolism

CYP1A2-inhibitor:	0.071
CYP1A2-substrate:	0.164
CYP2C19-inhibitor:	0.251
CYP2C19-substrate:	0.044
CYP2C9-inhibitor:	0.103
CYP2C9-substrate:	0.999
CYP2D6-inhibitor:	0.95
CYP2D6-substrate:	0.913
CYP3A4-inhibitor:	0.81
CYP3A4-substrate:	0.076

ADMET: Excretion

Clearance (CL):	2.804
Half-life (T1/2):	0.175

ADMET: Toxicity

hERG Blockers:	0.877
Human Hepatotoxicity (H-HT):	0.03
Drug-inuced Liver Injury (DILI):	0.337
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.008
Skin Sensitization:	0.98
Carcinogencity:	0.043
Eye Corrosion:	0.006
Eye Irritation:	0.266
Respiratory Toxicity:	0.584

Download Data

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

Natural Product: NPC476659

Natural Product ID:	NPC476659
*Common Name:**	1,3-dihydroxypropan-2-yl (5E,7E,23E,25E)-tetratriaconta-5,7,23,25-tetraenoate
IUPAC Name:	1,3-dihydroxypropan-2-yl (5E,7E,23E,25E)-tetratriaconta-5,7,23,25-tetraenoate
Synonyms:
Standard InCHIKey:	MOLXGYVCJRDZJM-NTPDKBNGSA-N
Standard InCHI:	InChI=1S/C37H66O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-29-30-31-32-33-37(40)41-36(34-38)35-39/h9-12,27-30,36,38-39H,2-8,13-26,31-35H2,1H3/b10-9+,12-11+,28-27+,30-29+
SMILES:	CCCCCCCC/C=C/C=C/CCCCCCCCCCCCCC/C=C/C=C/CCCC(=O)OC(CO)CO
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	76331186
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000175] Glycerolipids [CHEMONTID:0003808] Monoradylglycerols [CHEMONTID:0001133] Monoacylglycerols [CHEMONTID:0001603] 2-monoacylglycerols

*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
NPO33615	Aspergillus sp. MF-93	Species	Aspergillaceae	Eukaryota	n.a.	Quan-Zhou Gulf, Fujian Province, China	2002	PMID[18823067]

☑ 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
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT786	Organism	Tobacco mosaic virus	Tobacco mosaic virus	Inhibition	=	14.3	%	PMID[18823067]

☑ 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 NPC476659 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	158
0.1-0.2	1951
0.2-0.3	8883
0.3-0.4	17507
0.4-0.5	9668
0.5-0.6	3516
0.6-0.7	847
0.7-0.8	132
0.8-0.85	8
0.85-0.9	12
0.9-0.95	9
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC476656
0.9836	High Similarity	NPC476657
0.9836	High Similarity	NPC476654
0.9836	High Similarity	NPC476655
0.9672	High Similarity	NPC476658
0.9385	High Similarity	NPC476660
0.9231	High Similarity	NPC473772
0.918	High Similarity	NPC81896
0.918	High Similarity	NPC321919
0.9077	High Similarity	NPC473559
0.9077	High Similarity	NPC48218
0.9077	High Similarity	NPC141481
0.9077	High Similarity	NPC324981
0.8923	High Similarity	NPC473829
0.8923	High Similarity	NPC127091
0.8923	High Similarity	NPC475443
0.8923	High Similarity	NPC330426
0.8923	High Similarity	NPC148192
0.8923	High Similarity	NPC271921
0.8923	High Similarity	NPC22101
0.8923	High Similarity	NPC104537
0.8788	High Similarity	NPC273508
0.8788	High Similarity	NPC209327
0.8696	High Similarity	NPC474321
0.8438	Intermediate Similarity	NPC321838
0.8387	Intermediate Similarity	NPC323436
0.8308	Intermediate Similarity	NPC54925
0.8261	Intermediate Similarity	NPC42526
0.8209	Intermediate Similarity	NPC83965
0.8088	Intermediate Similarity	NPC25298
0.8088	Intermediate Similarity	NPC478100
0.806	Intermediate Similarity	NPC176215
0.806	Intermediate Similarity	NPC296436
0.8	Intermediate Similarity	NPC328311
0.8	Intermediate Similarity	NPC327112
0.7945	Intermediate Similarity	NPC470899
0.7941	Intermediate Similarity	NPC478101
0.7879	Intermediate Similarity	NPC320305
0.7879	Intermediate Similarity	NPC201939
0.7879	Intermediate Similarity	NPC328776
0.7857	Intermediate Similarity	NPC130618
0.7846	Intermediate Similarity	NPC322186
0.7846	Intermediate Similarity	NPC329249
0.7826	Intermediate Similarity	NPC473357
0.7826	Intermediate Similarity	NPC193029
0.7826	Intermediate Similarity	NPC26500
0.7826	Intermediate Similarity	NPC99619
0.7826	Intermediate Similarity	NPC478097
0.7812	Intermediate Similarity	NPC323498
0.7812	Intermediate Similarity	NPC323597
0.7812	Intermediate Similarity	NPC211752
0.7794	Intermediate Similarity	NPC136164
0.7794	Intermediate Similarity	NPC255863
0.7794	Intermediate Similarity	NPC326268
0.7794	Intermediate Similarity	NPC318420
0.7794	Intermediate Similarity	NPC245947
0.7778	Intermediate Similarity	NPC470435
0.7727	Intermediate Similarity	NPC243532
0.7662	Intermediate Similarity	NPC21693
0.7662	Intermediate Similarity	NPC236649
0.7656	Intermediate Similarity	NPC327388
0.7647	Intermediate Similarity	NPC328089
0.7647	Intermediate Similarity	NPC68343
0.7632	Intermediate Similarity	NPC263574
0.7632	Intermediate Similarity	NPC469747
0.7619	Intermediate Similarity	NPC137538
0.7612	Intermediate Similarity	NPC113293
0.7606	Intermediate Similarity	NPC470436
0.76	Intermediate Similarity	NPC110813
0.7576	Intermediate Similarity	NPC322002
0.7576	Intermediate Similarity	NPC318306
0.7568	Intermediate Similarity	NPC260396
0.7541	Intermediate Similarity	NPC59051
0.7536	Intermediate Similarity	NPC478098
0.7536	Intermediate Similarity	NPC478099
0.7534	Intermediate Similarity	NPC325627
0.75	Intermediate Similarity	NPC11796
0.75	Intermediate Similarity	NPC218817
0.75	Intermediate Similarity	NPC133377
0.75	Intermediate Similarity	NPC52264
0.7468	Intermediate Similarity	NPC156089
0.7468	Intermediate Similarity	NPC473500
0.7468	Intermediate Similarity	NPC470313
0.7468	Intermediate Similarity	NPC38295
0.7467	Intermediate Similarity	NPC190400
0.7467	Intermediate Similarity	NPC49392
0.7432	Intermediate Similarity	NPC107654
0.7429	Intermediate Similarity	NPC146811
0.7403	Intermediate Similarity	NPC1180
0.7397	Intermediate Similarity	NPC477981
0.7397	Intermediate Similarity	NPC477983
0.7397	Intermediate Similarity	NPC320119
0.7391	Intermediate Similarity	NPC475221
0.7385	Intermediate Similarity	NPC18951
0.7361	Intermediate Similarity	NPC475982
0.7361	Intermediate Similarity	NPC236208
0.7361	Intermediate Similarity	NPC143396
0.7324	Intermediate Similarity	NPC49863
0.7313	Intermediate Similarity	NPC222852
0.7302	Intermediate Similarity	NPC92114
0.7297	Intermediate Similarity	NPC284006
0.7297	Intermediate Similarity	NPC329890
0.7297	Intermediate Similarity	NPC329914
0.7297	Intermediate Similarity	NPC326024
0.7286	Intermediate Similarity	NPC323045
0.7286	Intermediate Similarity	NPC317881
0.7286	Intermediate Similarity	NPC320642
0.7273	Intermediate Similarity	NPC182292
0.7273	Intermediate Similarity	NPC317263
0.7273	Intermediate Similarity	NPC44542
0.7262	Intermediate Similarity	NPC313670
0.726	Intermediate Similarity	NPC473361
0.726	Intermediate Similarity	NPC476012
0.726	Intermediate Similarity	NPC329904
0.726	Intermediate Similarity	NPC476037
0.725	Intermediate Similarity	NPC253801
0.7246	Intermediate Similarity	NPC29697
0.7231	Intermediate Similarity	NPC128061
0.7231	Intermediate Similarity	NPC200845
0.7231	Intermediate Similarity	NPC28779
0.7231	Intermediate Similarity	NPC228473
0.7231	Intermediate Similarity	NPC223677
0.7231	Intermediate Similarity	NPC10316
0.7213	Intermediate Similarity	NPC91495
0.72	Intermediate Similarity	NPC227396
0.72	Intermediate Similarity	NPC160540
0.72	Intermediate Similarity	NPC315843
0.7183	Intermediate Similarity	NPC328653
0.7179	Intermediate Similarity	NPC470149
0.7179	Intermediate Similarity	NPC470148
0.7164	Intermediate Similarity	NPC469373
0.7162	Intermediate Similarity	NPC293114
0.716	Intermediate Similarity	NPC163093
0.7143	Intermediate Similarity	NPC470320
0.7125	Intermediate Similarity	NPC65930
0.7125	Intermediate Similarity	NPC94875
0.7125	Intermediate Similarity	NPC180363
0.7125	Intermediate Similarity	NPC145914
0.7125	Intermediate Similarity	NPC473529
0.7125	Intermediate Similarity	NPC473780
0.7125	Intermediate Similarity	NPC475159
0.7125	Intermediate Similarity	NPC11332
0.7125	Intermediate Similarity	NPC329829
0.7125	Intermediate Similarity	NPC73310
0.7125	Intermediate Similarity	NPC131002
0.7125	Intermediate Similarity	NPC473712
0.7123	Intermediate Similarity	NPC317583
0.7121	Intermediate Similarity	NPC325977
0.7121	Intermediate Similarity	NPC477201
0.7105	Intermediate Similarity	NPC473948
0.7101	Intermediate Similarity	NPC40082
0.7101	Intermediate Similarity	NPC325929
0.7101	Intermediate Similarity	NPC66460
0.7101	Intermediate Similarity	NPC64971
0.7101	Intermediate Similarity	NPC271282
0.7093	Intermediate Similarity	NPC478036
0.7093	Intermediate Similarity	NPC478037
0.7089	Intermediate Similarity	NPC133226
0.7089	Intermediate Similarity	NPC200446
0.7089	Intermediate Similarity	NPC103634
0.7089	Intermediate Similarity	NPC470147
0.7077	Intermediate Similarity	NPC87564
0.7077	Intermediate Similarity	NPC53463
0.7077	Intermediate Similarity	NPC261831
0.7077	Intermediate Similarity	NPC320588
0.7077	Intermediate Similarity	NPC25417
0.7077	Intermediate Similarity	NPC6095
0.7077	Intermediate Similarity	NPC154245
0.7077	Intermediate Similarity	NPC469937
0.7077	Intermediate Similarity	NPC32467
0.7077	Intermediate Similarity	NPC424
0.7077	Intermediate Similarity	NPC23155
0.7077	Intermediate Similarity	NPC322461
0.7077	Intermediate Similarity	NPC281972
0.7077	Intermediate Similarity	NPC88966
0.7077	Intermediate Similarity	NPC290563
0.7077	Intermediate Similarity	NPC85813
0.7073	Intermediate Similarity	NPC471567
0.7073	Intermediate Similarity	NPC322529
0.7073	Intermediate Similarity	NPC120398
0.7073	Intermediate Similarity	NPC477013
0.7073	Intermediate Similarity	NPC475206
0.7073	Intermediate Similarity	NPC477014
0.7059	Intermediate Similarity	NPC473311
0.7051	Intermediate Similarity	NPC473471
0.7051	Intermediate Similarity	NPC248775
0.7051	Intermediate Similarity	NPC221095
0.7051	Intermediate Similarity	NPC279214
0.7042	Intermediate Similarity	NPC323477
0.7042	Intermediate Similarity	NPC19769
0.7037	Intermediate Similarity	NPC229799
0.7037	Intermediate Similarity	NPC286770
0.7037	Intermediate Similarity	NPC144415
0.7037	Intermediate Similarity	NPC178758
0.7037	Intermediate Similarity	NPC196102
0.7037	Intermediate Similarity	NPC284472
0.7024	Intermediate Similarity	NPC201046
0.7015	Intermediate Similarity	NPC472445
0.7015	Intermediate Similarity	NPC225929
0.7013	Intermediate Similarity	NPC188860

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 NPC476659 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	123
0.1-0.2	2563
0.2-0.3	3974
0.3-0.4	1784
0.4-0.5	568
0.5-0.6	95
0.6-0.7	36
0.7-0.8	7
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
0.8	Intermediate Similarity	NPD4246	Clinical (unspecified phase)
0.7969	Intermediate Similarity	NPD6109	Phase 1
0.791	Intermediate Similarity	NPD3197	Phase 1
0.7324	Intermediate Similarity	NPD4247	Clinical (unspecified phase)
0.7213	Intermediate Similarity	NPD5343	Approved
0.7176	Intermediate Similarity	NPD7983	Approved
0.7077	Intermediate Similarity	NPD3196	Approved
0.7077	Intermediate Similarity	NPD3728	Approved
0.7077	Intermediate Similarity	NPD4266	Approved
0.7077	Intermediate Similarity	NPD3730	Approved
0.7077	Intermediate Similarity	NPD3195	Phase 2
0.7077	Intermediate Similarity	NPD3194	Approved
0.6923	Remote Similarity	NPD3172	Approved
0.6885	Remote Similarity	NPD4222	Approved
0.6885	Remote Similarity	NPD39	Approved
0.6875	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.686	Remote Similarity	NPD7838	Discovery
0.6825	Remote Similarity	NPD3173	Approved
0.6721	Remote Similarity	NPD6097	Approved
0.6721	Remote Similarity	NPD6096	Approved
0.6707	Remote Similarity	NPD6435	Approved
0.6627	Remote Similarity	NPD7154	Phase 3
0.6625	Remote Similarity	NPD4268	Approved
0.6625	Remote Similarity	NPD4271	Approved
0.6615	Remote Similarity	NPD29	Approved
0.6615	Remote Similarity	NPD28	Approved
0.6557	Remote Similarity	NPD5326	Phase 3
0.6552	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6552	Remote Similarity	NPD6101	Approved
0.6477	Remote Similarity	NPD6698	Approved
0.6477	Remote Similarity	NPD46	Approved
0.6463	Remote Similarity	NPD4819	Approved
0.6463	Remote Similarity	NPD4820	Approved
0.6463	Remote Similarity	NPD4822	Approved
0.6463	Remote Similarity	NPD5368	Approved
0.6463	Remote Similarity	NPD4821	Approved
0.642	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6404	Remote Similarity	NPD6411	Approved
0.6386	Remote Similarity	NPD5369	Approved
0.6349	Remote Similarity	NPD3174	Discontinued
0.6333	Remote Similarity	NPD5779	Approved
0.6333	Remote Similarity	NPD5778	Approved
0.6322	Remote Similarity	NPD4251	Approved
0.6322	Remote Similarity	NPD4250	Approved
0.6304	Remote Similarity	NPD7839	Suspended
0.6265	Remote Similarity	NPD4252	Approved
0.6265	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.625	Remote Similarity	NPD8039	Approved
0.6235	Remote Similarity	NPD5362	Discontinued
0.6222	Remote Similarity	NPD7637	Suspended
0.6207	Remote Similarity	NPD4249	Approved
0.6197	Remote Similarity	NPD585	Clinical (unspecified phase)
0.617	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6154	Remote Similarity	NPD622	Approved
0.6154	Remote Similarity	NPD6125	Clinical (unspecified phase)
0.6119	Remote Similarity	NPD6927	Phase 3
0.6118	Remote Similarity	NPD4269	Approved
0.6118	Remote Similarity	NPD4270	Approved
0.6098	Remote Similarity	NPD4756	Discovery
0.6047	Remote Similarity	NPD5332	Approved
0.6047	Remote Similarity	NPD5331	Approved
0.6024	Remote Similarity	NPD3732	Approved
0.6023	Remote Similarity	NPD5786	Approved
0.6	Remote Similarity	NPD4790	Discontinued
0.5976	Remote Similarity	NPD819	Approved
0.5976	Remote Similarity	NPD818	Approved
0.593	Remote Similarity	NPD5209	Approved
0.5909	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5909	Remote Similarity	NPD5363	Approved
0.5824	Remote Similarity	NPD5370	Suspended
0.5795	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5795	Remote Similarity	NPD5766	Clinical (unspecified phase)
0.5789	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.5761	Remote Similarity	NPD5785	Approved
0.5714	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5699	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.5692	Remote Similarity	NPD2699	Approved
0.5682	Remote Similarity	NPD6110	Phase 1
0.5673	Remote Similarity	NPD8413	Clinical (unspecified phase)
0.567	Remote Similarity	NPD4225	Approved
0.5667	Remote Similarity	NPD6422	Discontinued
0.5658	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.5641	Remote Similarity	NPD3704	Approved
0.5638	Remote Similarity	NPD5781	Clinical (unspecified phase)
0.5634	Remote Similarity	NPD3729	Clinical (unspecified phase)
0.5625	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5612	Remote Similarity	NPD7798	Approved
0.5606	Remote Similarity	NPD4265	Approved
0.5604	Remote Similarity	NPD7524	Approved
0.56	Remote Similarity	NPD6647	Phase 2

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