NPASS Compound

Structure

CID54460 OpenBabel06191715392D 42 41 0 0 1 0 0 0 0 0999 V2000 11.2942 -4.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5000 -9.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2942 -5.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4282 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5622 -5.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6962 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8301 -5.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -8.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0000 -8.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5000 -7.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9641 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5000 -9.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -7.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0981 -5.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5000 -9.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -6.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2321 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0000 -9.9282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3660 -5.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0000 -4.7321 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -7.0000 -9.9282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 -7.5000 -10.7942 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 -6.4641 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6340 -6.0981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5000 -2.1340 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 -7.5000 -9.0622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -5.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -3.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -4.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5000 -5.5981 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 1 6 1 0 0 0 0 2 30 1 0 0 0 0 3 30 1 0 0 0 0 4 30 1 0 0 0 0 5 36 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 10 1 0 0 0 0 10 14 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 12 15 1 0 0 0 0 13 16 1 0 0 0 0 14 17 1 0 0 0 0 15 18 1 0 0 0 0 16 19 1 0 0 0 0 17 20 1 0 0 0 0 18 21 1 0 0 0 0 19 23 1 0 0 0 0 20 25 1 0 0 0 0 21 29 1 0 0 0 0 22 24 1 0 0 0 0 22 30 1 0 0 0 0 23 37 1 0 0 0 0 24 38 1 0 0 0 0 25 41 1 0 0 0 0 26 28 1 0 0 0 0 26 37 1 0 0 0 0 27 28 1 0 0 0 0 27 39 1 0 0 0 0 28 40 1 0 0 0 0 29 31 2 0 0 0 0 29 36 1 0 0 0 0 32 41 2 0 0 0 0 33 41 1 0 0 0 0 34 42 2 0 0 0 0 35 42 1 0 0 0 0 38 42 1 0 0 0 0 39 42 1 0 0 0 0 40 41 1 0 0 0 0 M CHG 2 30 1 35 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	645.38
Volume:	646.057
LogP:	1.667
LogD:	1.408
LogS:	0.223
# Rotatable Bonds:	31
TPSA:	137.49
# H-Bond Aceptor:	11
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.037
Synthetic Accessibility Score:	4.566
Fsp3:	0.966
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:	-5.452
MDCK Permeability:	2.7373283955967054e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.066
Human Intestinal Absorption (HIA):	0.765
20% Bioavailability (F20%):	0.702
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	88.42325592041016%
Volume Distribution (VD):	0.509
Pgp-substrate:	9.738300323486328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.857
CYP2C19-inhibitor:	0.077
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.099
CYP2C9-substrate:	0.717
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.157
CYP3A4-inhibitor:	0.485
CYP3A4-substrate:	0.01

ADMET: Excretion

Clearance (CL):	1.962
Half-life (T1/2):	0.826

ADMET: Toxicity

hERG Blockers:	0.243
Human Hepatotoxicity (H-HT):	0.186
Drug-inuced Liver Injury (DILI):	0.004
AMES Toxicity:	0.092
Rat Oral Acute Toxicity:	0.004
Maximum Recommended Daily Dose:	0.919
Skin Sensitization:	0.926
Carcinogencity:	0.452
Eye Corrosion:	0.02
Eye Irritation:	0.034
Respiratory Toxicity:	0.412

Download Data

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

Natural Product: NPC54460

Natural Product ID:	NPC54460
*Common Name:**	Ester Of Phospholipid
IUPAC Name:	[2-[decyl(hydroxy)phosphoryl]oxy-3-(10-methoxy-10-oxodecoxy)propyl] 2-(trimethylazaniumyl)ethyl phosphate
Synonyms:
Standard InCHIKey:	GUBMPMUEZUKTNI-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C29H61NO10P2/c1-6-7-8-9-10-14-17-20-25-41(32,33)40-28(27-39-42(34,35)38-24-22-30(2,3)4)26-37-23-19-16-13-11-12-15-18-21-29(31)36-5/h28H,6-27H2,1-5H3,(H-,32,33,34,35)
SMILES:	CCCCCCCCCCP(=O)(O)OC(COCCCCCCCCCC(=O)OC)COP(=O)([O-])OCC[N+](C)(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL85557
PubChem CID:	44319037
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000256] Glycerophospholipids [CHEMONTID:0002213] Glycerophosphocholines

*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
NPO13291	Changium smyrnioides	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13291	Changium smyrnioides	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13291	Changium smyrnioides	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

☑ 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
IC50	1
Ki	1

Activity Type	# Activity
Individual Protein	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3178	Individual Protein	Lysosomal phospholipase A2	Homo sapiens	IC50	=	9750000.0	nM	PMID[500664]
NPT27	Others	Unspecified		Ki	=	10000.0	nM	PMID[500663]

☑ 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 NPC54460 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	412
0.1-0.2	8607
0.2-0.3	21082
0.3-0.4	10929
0.4-0.5	1430
0.5-0.6	195
0.6-0.7	22
0.7-0.8	10
0.8-0.85	1
0.85-0.9	6
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9254	High Similarity	NPC224700
0.9254	High Similarity	NPC320663
0.8986	High Similarity	NPC114640
0.8986	High Similarity	NPC126366
0.8986	High Similarity	NPC33267
0.8986	High Similarity	NPC170963
0.8986	High Similarity	NPC324165
0.8986	High Similarity	NPC169976
0.8378	Intermediate Similarity	NPC330017
0.8052	Intermediate Similarity	NPC474702
0.7654	Intermediate Similarity	NPC196102
0.7654	Intermediate Similarity	NPC178758
0.7536	Intermediate Similarity	NPC474627
0.7536	Intermediate Similarity	NPC201338
0.7536	Intermediate Similarity	NPC328786
0.7342	Intermediate Similarity	NPC325936
0.726	Intermediate Similarity	NPC326651
0.726	Intermediate Similarity	NPC325117
0.726	Intermediate Similarity	NPC322319
0.7027	Intermediate Similarity	NPC238646
0.6795	Remote Similarity	NPC321873
0.6795	Remote Similarity	NPC470268
0.6765	Remote Similarity	NPC473872
0.6716	Remote Similarity	NPC55678
0.6571	Remote Similarity	NPC469937
0.6571	Remote Similarity	NPC53463
0.6571	Remote Similarity	NPC23155
0.6571	Remote Similarity	NPC320588
0.6429	Remote Similarity	NPC473984
0.642	Remote Similarity	NPC305223
0.6377	Remote Similarity	NPC287811
0.6237	Remote Similarity	NPC329906
0.6212	Remote Similarity	NPC47363
0.6212	Remote Similarity	NPC287231
0.6133	Remote Similarity	NPC470363
0.6087	Remote Similarity	NPC26253
0.6049	Remote Similarity	NPC127145
0.6049	Remote Similarity	NPC475930
0.6024	Remote Similarity	NPC208657
0.5976	Remote Similarity	NPC474674
0.5942	Remote Similarity	NPC106872
0.5926	Remote Similarity	NPC28348
0.5926	Remote Similarity	NPC474299
0.5926	Remote Similarity	NPC474298
0.5926	Remote Similarity	NPC473985
0.5926	Remote Similarity	NPC475808
0.5909	Remote Similarity	NPC236579
0.5909	Remote Similarity	NPC203531
0.5854	Remote Similarity	NPC474675
0.5854	Remote Similarity	NPC137620
0.5802	Remote Similarity	NPC206601
0.5797	Remote Similarity	NPC328497
0.5797	Remote Similarity	NPC324004
0.5775	Remote Similarity	NPC90904
0.5761	Remote Similarity	NPC83839
0.5758	Remote Similarity	NPC53541
0.5714	Remote Similarity	NPC474403
0.5714	Remote Similarity	NPC477641
0.5714	Remote Similarity	NPC319131
0.5714	Remote Similarity	NPC320865
0.5714	Remote Similarity	NPC477643
0.5696	Remote Similarity	NPC54925
0.5663	Remote Similarity	NPC285003
0.5663	Remote Similarity	NPC241265
0.5652	Remote Similarity	NPC145045
0.5652	Remote Similarity	NPC105329
0.5652	Remote Similarity	NPC63182
0.5652	Remote Similarity	NPC12438
0.5652	Remote Similarity	NPC30195
0.5652	Remote Similarity	NPC52700
0.5616	Remote Similarity	NPC35816
0.5616	Remote Similarity	NPC325180
0.561	Remote Similarity	NPC104537
0.561	Remote Similarity	NPC473829
0.561	Remote Similarity	NPC271921
0.561	Remote Similarity	NPC127091
0.561	Remote Similarity	NPC148192
0.561	Remote Similarity	NPC469925
0.561	Remote Similarity	NPC330426
0.561	Remote Similarity	NPC22101
0.561	Remote Similarity	NPC475443
0.5606	Remote Similarity	NPC161097
0.5606	Remote Similarity	NPC165533
0.5606	Remote Similarity	NPC256163
0.5606	Remote Similarity	NPC250028
0.5606	Remote Similarity	NPC12156
0.5606	Remote Similarity	NPC28598
0.5606	Remote Similarity	NPC149299
0.5606	Remote Similarity	NPC40597
0.5604	Remote Similarity	NPC47135

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 NPC54460 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	408
0.1-0.2	4054
0.2-0.3	3336
0.3-0.4	1054
0.4-0.5	236
0.5-0.6	51
0.6-0.7	8
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	2
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9403	High Similarity	NPD8277	Approved
0.9254	High Similarity	NPD8278	Approved
0.7727	Intermediate Similarity	NPD6950	Discontinued
0.6849	Remote Similarity	NPD4283	Discontinued
0.6757	Remote Similarity	NPD7347	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD4840	Approved
0.6667	Remote Similarity	NPD6125	Clinical (unspecified phase)
0.6571	Remote Similarity	NPD3728	Approved
0.6571	Remote Similarity	NPD3730	Approved
0.6212	Remote Similarity	NPD2699	Approved
0.6104	Remote Similarity	NPD1151	Approved
0.6098	Remote Similarity	NPD6704	Discontinued
0.6071	Remote Similarity	NPD376	Approved
0.6071	Remote Similarity	NPD11	Approved
0.6049	Remote Similarity	NPD3725	Approved
0.6049	Remote Similarity	NPD3726	Approved
0.6027	Remote Similarity	NPD6706	Discontinued
0.5946	Remote Similarity	NPD6439	Phase 3
0.5875	Remote Similarity	NPD5380	Approved
0.5783	Remote Similarity	NPD7535	Discontinued
0.5769	Remote Similarity	NPD6949	Clinical (unspecified phase)
0.5714	Remote Similarity	NPD2256	Clinical (unspecified phase)
0.5676	Remote Similarity	NPD7756	Clinical (unspecified phase)
0.5616	Remote Similarity	NPD9660	Approved
0.5604	Remote Similarity	NPD883	Phase 2
0.5604	Remote Similarity	NPD882	Phase 2
0.5604	Remote Similarity	NPD7345	Approved
0.56	Remote Similarity	NPD9659	Approved

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