NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	354.28
Volume:	399.024
LogP:	4.42
LogD:	3.724
LogS:	-3.835
# Rotatable Bonds:	18
TPSA:	66.76
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.226
Synthetic Accessibility Score:	2.982
Fsp3:	0.762
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.652
MDCK Permeability:	3.933814150514081e-05
Pgp-inhibitor:	0.206
Pgp-substrate:	0.019
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.753
30% Bioavailability (F30%):	0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.338
Plasma Protein Binding (PPB):	95.61412048339844%
Volume Distribution (VD):	0.493
Pgp-substrate:	1.9675078392028809%

ADMET: Metabolism

CYP1A2-inhibitor:	0.673
CYP1A2-substrate:	0.187
CYP2C19-inhibitor:	0.526
CYP2C19-substrate:	0.09
CYP2C9-inhibitor:	0.418
CYP2C9-substrate:	0.985
CYP2D6-inhibitor:	0.374
CYP2D6-substrate:	0.795
CYP3A4-inhibitor:	0.913
CYP3A4-substrate:	0.129

ADMET: Excretion

Clearance (CL):	5.604
Half-life (T1/2):	0.708

ADMET: Toxicity

hERG Blockers:	0.31
Human Hepatotoxicity (H-HT):	0.04
Drug-inuced Liver Injury (DILI):	0.035
AMES Toxicity:	0.054
Rat Oral Acute Toxicity:	0.011
Maximum Recommended Daily Dose:	0.012
Skin Sensitization:	0.947
Carcinogencity:	0.162
Eye Corrosion:	0.005
Eye Irritation:	0.104
Respiratory Toxicity:	0.267

Download Data

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

Natural Product: NPC476654

Natural Product ID:	NPC476654
*Common Name:**	2,3-dihydroxypropyl (5E,7E)-octadeca-5,7-dienoate
IUPAC Name:	2,3-dihydroxypropyl (5E,7E)-octadeca-5,7-dienoate
Synonyms:
Standard InCHIKey:	VIJAZCBOAKGHAD-LDHFCIDVSA-N
Standard InCHI:	InChI=1S/C21H38O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h11-14,20,22-23H,2-10,15-19H2,1H3/b12-11+,14-13+
SMILES:	CCCCCCCCCC/C=C/C=C/CCCC(=O)OCC(CO)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	76316612
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000504] Lineolic acids and derivatives

*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	=	12.5	%	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 NPC476654 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	154
0.1-0.2	1899
0.2-0.3	8735
0.3-0.4	17511
0.4-0.5	9677
0.5-0.6	3661
0.6-0.7	858
0.7-0.8	162
0.8-0.85	13
0.85-0.9	11
0.9-0.95	11
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC476655
1.0	High Similarity	NPC476657
0.9836	High Similarity	NPC476659
0.9836	High Similarity	NPC476656
0.9508	High Similarity	NPC476658
0.9333	High Similarity	NPC81896
0.9333	High Similarity	NPC321919
0.9231	High Similarity	NPC476660
0.9077	High Similarity	NPC473772
0.9062	High Similarity	NPC127091
0.9062	High Similarity	NPC22101
0.9062	High Similarity	NPC104537
0.9062	High Similarity	NPC148192
0.9062	High Similarity	NPC330426
0.9062	High Similarity	NPC271921
0.8923	High Similarity	NPC141481
0.8923	High Similarity	NPC48218
0.8923	High Similarity	NPC273508
0.8923	High Similarity	NPC324981
0.8923	High Similarity	NPC473559
0.8923	High Similarity	NPC209327
0.8824	High Similarity	NPC474321
0.8769	High Similarity	NPC473829
0.8769	High Similarity	NPC475443
0.8571	High Similarity	NPC321838
0.8525	High Similarity	NPC323436
0.8382	Intermediate Similarity	NPC42526
0.8333	Intermediate Similarity	NPC83965
0.8209	Intermediate Similarity	NPC478100
0.8209	Intermediate Similarity	NPC25298
0.8182	Intermediate Similarity	NPC296436
0.8182	Intermediate Similarity	NPC176215
0.8154	Intermediate Similarity	NPC54925
0.8125	Intermediate Similarity	NPC327112
0.8125	Intermediate Similarity	NPC328311
0.806	Intermediate Similarity	NPC478101
0.8056	Intermediate Similarity	NPC470899
0.8	Intermediate Similarity	NPC201939
0.8	Intermediate Similarity	NPC320305
0.8	Intermediate Similarity	NPC328776
0.7971	Intermediate Similarity	NPC130618
0.7969	Intermediate Similarity	NPC322186
0.7969	Intermediate Similarity	NPC329249
0.7941	Intermediate Similarity	NPC99619
0.7941	Intermediate Similarity	NPC478097
0.7941	Intermediate Similarity	NPC26500
0.7937	Intermediate Similarity	NPC323498
0.7937	Intermediate Similarity	NPC323597
0.7937	Intermediate Similarity	NPC211752
0.791	Intermediate Similarity	NPC255863
0.791	Intermediate Similarity	NPC318420
0.791	Intermediate Similarity	NPC245947
0.791	Intermediate Similarity	NPC326268
0.791	Intermediate Similarity	NPC136164
0.7887	Intermediate Similarity	NPC470435
0.7846	Intermediate Similarity	NPC243532
0.7778	Intermediate Similarity	NPC327388
0.7761	Intermediate Similarity	NPC328089
0.7761	Intermediate Similarity	NPC68343
0.7742	Intermediate Similarity	NPC137538
0.7733	Intermediate Similarity	NPC263574
0.7733	Intermediate Similarity	NPC469747
0.7727	Intermediate Similarity	NPC113293
0.7714	Intermediate Similarity	NPC470436
0.7692	Intermediate Similarity	NPC322002
0.7692	Intermediate Similarity	NPC318306
0.7681	Intermediate Similarity	NPC193029
0.7681	Intermediate Similarity	NPC473357
0.7671	Intermediate Similarity	NPC260396
0.7667	Intermediate Similarity	NPC59051
0.7647	Intermediate Similarity	NPC478099
0.7647	Intermediate Similarity	NPC478098
0.7639	Intermediate Similarity	NPC325627
0.7619	Intermediate Similarity	NPC52264
0.76	Intermediate Similarity	NPC218817
0.76	Intermediate Similarity	NPC11796
0.7568	Intermediate Similarity	NPC49392
0.7568	Intermediate Similarity	NPC190400
0.7536	Intermediate Similarity	NPC146811
0.7534	Intermediate Similarity	NPC107654
0.7532	Intermediate Similarity	NPC236649
0.7532	Intermediate Similarity	NPC21693
0.75	Intermediate Similarity	NPC320119
0.75	Intermediate Similarity	NPC477981
0.75	Intermediate Similarity	NPC477983
0.75	Intermediate Similarity	NPC1180
0.75	Intermediate Similarity	NPC475221
0.75	Intermediate Similarity	NPC18951
0.7467	Intermediate Similarity	NPC110813
0.7465	Intermediate Similarity	NPC143396
0.7465	Intermediate Similarity	NPC475982
0.7465	Intermediate Similarity	NPC236208
0.7429	Intermediate Similarity	NPC49863
0.7424	Intermediate Similarity	NPC222852
0.7419	Intermediate Similarity	NPC92114
0.7397	Intermediate Similarity	NPC329890
0.7397	Intermediate Similarity	NPC326024
0.7397	Intermediate Similarity	NPC284006
0.7397	Intermediate Similarity	NPC329914
0.7391	Intermediate Similarity	NPC317881
0.7391	Intermediate Similarity	NPC323045
0.7391	Intermediate Similarity	NPC320642
0.7385	Intermediate Similarity	NPC44542
0.7368	Intermediate Similarity	NPC182292
0.7368	Intermediate Similarity	NPC317263
0.7368	Intermediate Similarity	NPC133377
0.7361	Intermediate Similarity	NPC476012
0.7361	Intermediate Similarity	NPC476037
0.7361	Intermediate Similarity	NPC329904
0.7361	Intermediate Similarity	NPC473361
0.7353	Intermediate Similarity	NPC29697
0.7344	Intermediate Similarity	NPC128061
0.7344	Intermediate Similarity	NPC200845
0.7344	Intermediate Similarity	NPC223677
0.7344	Intermediate Similarity	NPC228473
0.7344	Intermediate Similarity	NPC10316
0.7344	Intermediate Similarity	NPC28779
0.7342	Intermediate Similarity	NPC156089
0.7342	Intermediate Similarity	NPC473500
0.7342	Intermediate Similarity	NPC38295
0.7342	Intermediate Similarity	NPC470313
0.7333	Intermediate Similarity	NPC91495
0.7297	Intermediate Similarity	NPC160540
0.7297	Intermediate Similarity	NPC227396
0.7297	Intermediate Similarity	NPC315843
0.7286	Intermediate Similarity	NPC328653
0.7273	Intermediate Similarity	NPC469373
0.726	Intermediate Similarity	NPC293114
0.7246	Intermediate Similarity	NPC470320
0.7231	Intermediate Similarity	NPC325977
0.7231	Intermediate Similarity	NPC477201
0.7222	Intermediate Similarity	NPC317583
0.7206	Intermediate Similarity	NPC325929
0.7206	Intermediate Similarity	NPC66460
0.7206	Intermediate Similarity	NPC271282
0.7206	Intermediate Similarity	NPC64971
0.7206	Intermediate Similarity	NPC40082
0.72	Intermediate Similarity	NPC473948
0.7188	Intermediate Similarity	NPC320588
0.7188	Intermediate Similarity	NPC261831
0.7188	Intermediate Similarity	NPC25417
0.7188	Intermediate Similarity	NPC290563
0.7188	Intermediate Similarity	NPC424
0.7188	Intermediate Similarity	NPC23155
0.7188	Intermediate Similarity	NPC85813
0.7188	Intermediate Similarity	NPC469937
0.7188	Intermediate Similarity	NPC281972
0.7188	Intermediate Similarity	NPC87564
0.7188	Intermediate Similarity	NPC32467
0.7188	Intermediate Similarity	NPC322461
0.7188	Intermediate Similarity	NPC88966
0.7188	Intermediate Similarity	NPC154245
0.7188	Intermediate Similarity	NPC6095
0.7188	Intermediate Similarity	NPC53463
0.7179	Intermediate Similarity	NPC200446
0.7179	Intermediate Similarity	NPC103634
0.7143	Intermediate Similarity	NPC19769
0.7143	Intermediate Similarity	NPC248775
0.7143	Intermediate Similarity	NPC473471
0.7143	Intermediate Similarity	NPC323477
0.7143	Intermediate Similarity	NPC473311
0.7143	Intermediate Similarity	NPC313670
0.7125	Intermediate Similarity	NPC196102
0.7125	Intermediate Similarity	NPC229799
0.7125	Intermediate Similarity	NPC286770
0.7125	Intermediate Similarity	NPC253801
0.7125	Intermediate Similarity	NPC284472
0.7125	Intermediate Similarity	NPC178758
0.7121	Intermediate Similarity	NPC472445
0.7121	Intermediate Similarity	NPC225929
0.7105	Intermediate Similarity	NPC188860
0.7089	Intermediate Similarity	NPC474894
0.7083	Intermediate Similarity	NPC477980
0.7083	Intermediate Similarity	NPC474823
0.7083	Intermediate Similarity	NPC63873
0.7067	Intermediate Similarity	NPC473489
0.7059	Intermediate Similarity	NPC122521
0.7059	Intermediate Similarity	NPC251042
0.7059	Intermediate Similarity	NPC174447
0.7059	Intermediate Similarity	NPC229252
0.7059	Intermediate Similarity	NPC143857
0.7051	Intermediate Similarity	NPC470149
0.7051	Intermediate Similarity	NPC209995
0.7051	Intermediate Similarity	NPC470148
0.7051	Intermediate Similarity	NPC471537
0.7051	Intermediate Similarity	NPC180725
0.7042	Intermediate Similarity	NPC276299
0.7042	Intermediate Similarity	NPC201356
0.7037	Intermediate Similarity	NPC163093
0.7031	Intermediate Similarity	NPC1813
0.7031	Intermediate Similarity	NPC71761
0.7031	Intermediate Similarity	NPC36061
0.7031	Intermediate Similarity	NPC294548
0.7031	Intermediate Similarity	NPC39633
0.7031	Intermediate Similarity	NPC139029
0.7031	Intermediate Similarity	NPC139545
0.7031	Intermediate Similarity	NPC284224
0.7031	Intermediate Similarity	NPC321062
0.7031	Intermediate Similarity	NPC309606
0.7031	Intermediate Similarity	NPC70387

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 NPC476654 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	122
0.1-0.2	2515
0.2-0.3	3972
0.3-0.4	1804
0.4-0.5	599
0.5-0.6	94
0.6-0.7	33
0.7-0.8	10
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8125	Intermediate Similarity	NPD4246	Clinical (unspecified phase)
0.8095	Intermediate Similarity	NPD6109	Phase 1
0.803	Intermediate Similarity	NPD3197	Phase 1
0.7429	Intermediate Similarity	NPD4247	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD5343	Approved
0.7188	Intermediate Similarity	NPD3194	Approved
0.7188	Intermediate Similarity	NPD3195	Phase 2
0.7188	Intermediate Similarity	NPD3728	Approved
0.7188	Intermediate Similarity	NPD3196	Approved
0.7188	Intermediate Similarity	NPD3730	Approved
0.7188	Intermediate Similarity	NPD4266	Approved
0.7059	Intermediate Similarity	NPD7983	Approved
0.7031	Intermediate Similarity	NPD3172	Approved
0.7	Intermediate Similarity	NPD4222	Approved
0.7	Intermediate Similarity	NPD39	Approved
0.6962	Remote Similarity	NPD5790	Clinical (unspecified phase)
0.6935	Remote Similarity	NPD3173	Approved
0.6833	Remote Similarity	NPD6097	Approved
0.6833	Remote Similarity	NPD6096	Approved
0.679	Remote Similarity	NPD6435	Approved
0.6744	Remote Similarity	NPD7838	Discovery
0.6719	Remote Similarity	NPD29	Approved
0.6719	Remote Similarity	NPD28	Approved
0.6709	Remote Similarity	NPD4268	Approved
0.6709	Remote Similarity	NPD4271	Approved
0.6707	Remote Similarity	NPD7154	Phase 3
0.6667	Remote Similarity	NPD5326	Phase 3
0.6628	Remote Similarity	NPD5764	Clinical (unspecified phase)
0.6628	Remote Similarity	NPD6101	Approved
0.6552	Remote Similarity	NPD6698	Approved
0.6552	Remote Similarity	NPD46	Approved
0.6543	Remote Similarity	NPD4820	Approved
0.6543	Remote Similarity	NPD5368	Approved
0.6543	Remote Similarity	NPD4822	Approved
0.6543	Remote Similarity	NPD4819	Approved
0.6543	Remote Similarity	NPD4821	Approved
0.65	Remote Similarity	NPD5784	Clinical (unspecified phase)
0.6477	Remote Similarity	NPD6411	Approved
0.6463	Remote Similarity	NPD5369	Approved
0.6452	Remote Similarity	NPD3174	Discontinued
0.6404	Remote Similarity	NPD5778	Approved
0.6404	Remote Similarity	NPD5779	Approved
0.6395	Remote Similarity	NPD4250	Approved
0.6395	Remote Similarity	NPD4251	Approved
0.6341	Remote Similarity	NPD4252	Approved
0.631	Remote Similarity	NPD5362	Discontinued
0.6292	Remote Similarity	NPD7637	Suspended
0.6286	Remote Similarity	NPD585	Clinical (unspecified phase)
0.6279	Remote Similarity	NPD4249	Approved
0.625	Remote Similarity	NPD6125	Clinical (unspecified phase)
0.625	Remote Similarity	NPD622	Approved
0.6212	Remote Similarity	NPD6927	Phase 3
0.6196	Remote Similarity	NPD7839	Suspended
0.619	Remote Similarity	NPD4270	Approved
0.619	Remote Similarity	NPD4269	Approved
0.6173	Remote Similarity	NPD4756	Discovery
0.6145	Remote Similarity	NPD8259	Clinical (unspecified phase)
0.6125	Remote Similarity	NPD8039	Approved
0.6118	Remote Similarity	NPD5332	Approved
0.6118	Remote Similarity	NPD5331	Approved
0.6098	Remote Similarity	NPD3732	Approved
0.6092	Remote Similarity	NPD5786	Approved
0.6071	Remote Similarity	NPD4790	Discontinued
0.6064	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6049	Remote Similarity	NPD818	Approved
0.6049	Remote Similarity	NPD819	Approved
0.6	Remote Similarity	NPD5209	Approved
0.5977	Remote Similarity	NPD5363	Approved
0.5977	Remote Similarity	NPD6082	Clinical (unspecified phase)
0.5889	Remote Similarity	NPD5370	Suspended
0.5867	Remote Similarity	NPD5325	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD6400	Clinical (unspecified phase)
0.5862	Remote Similarity	NPD5766	Clinical (unspecified phase)
0.5824	Remote Similarity	NPD5785	Approved
0.5789	Remote Similarity	NPD2685	Clinical (unspecified phase)
0.5781	Remote Similarity	NPD2699	Approved
0.5761	Remote Similarity	NPD4810	Clinical (unspecified phase)
0.5747	Remote Similarity	NPD6110	Phase 1
0.5733	Remote Similarity	NPD3210	Clinical (unspecified phase)
0.573	Remote Similarity	NPD6422	Discontinued
0.5729	Remote Similarity	NPD4225	Approved
0.5714	Remote Similarity	NPD3729	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD3704	Approved
0.5699	Remote Similarity	NPD5781	Clinical (unspecified phase)
0.5692	Remote Similarity	NPD4265	Approved
0.5684	Remote Similarity	NPD4792	Clinical (unspecified phase)
0.5672	Remote Similarity	NPD4220	Pre-registration
0.5667	Remote Similarity	NPD7524	Approved
0.5657	Remote Similarity	NPD6647	Phase 2
0.5644	Remote Similarity	NPD6685	Approved
0.5616	Remote Similarity	NPD69	Approved
0.5616	Remote Similarity	NPD9119	Approved
0.5612	Remote Similarity	NPD5344	Discontinued

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