NPASS Compound

Structure

NPC238646 OpenBabel07101718192D 33 32 0 0 1 0 0 0 0 0999 V2000 -15.5000 -9.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -15.5000 -10.7942 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 -9.5000 -7.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0000 -6.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5000 -7.3301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0000 -6.4641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0000 -8.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5000 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.0000 -8.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5000 -5.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5000 -9.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0000 -4.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.5000 -9.0622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0000 -4.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.0000 -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 -4.5000 -3.8660 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 -3.0000 -3.0000 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 -15.0000 -9.9282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0000 -3.0000 0.0000 C 0 0 2 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 -1.5000 -2.1340 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 -3.5000 -3.8660 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 0.0000 -3.0000 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 1 24 1 0 0 0 0 2 24 1 0 0 0 0 3 26 1 0 0 0 0 4 26 1 0 0 0 0 5 26 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 7 9 1 0 0 0 0 8 10 1 0 0 0 0 9 11 1 0 0 0 0 10 12 1 0 0 0 0 11 13 1 0 0 0 0 12 14 1 0 0 0 0 13 15 1 0 0 0 0 14 16 1 0 0 0 0 15 17 1 0 0 0 0 16 18 1 0 0 0 0 17 20 1 0 0 0 0 18 24 1 0 0 0 0 19 21 1 0 0 0 0 19 26 1 0 0 0 0 20 30 1 0 0 0 0 21 31 1 0 0 0 0 22 25 1 0 0 0 0 22 30 1 0 0 0 0 23 25 1 0 0 0 0 23 32 1 0 0 0 0 25 27 1 1 0 0 0 28 33 2 0 0 0 0 29 33 1 0 0 0 0 31 33 1 0 0 0 0 32 33 1 0 0 0 0 M CHG 2 26 1 29 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	495.37
Volume:	524.521
LogP:	2.744
LogD:	1.572
LogS:	-0.057
# Rotatable Bonds:	24
TPSA:	88.05
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	0
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.111
Synthetic Accessibility Score:	3.796
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-5.434
MDCK Permeability:	2.932019742729608e-05
Pgp-inhibitor:	0.016
Pgp-substrate:	0.504
Human Intestinal Absorption (HIA):	0.289
20% Bioavailability (F20%):	0.784
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	93.66498565673828%
Volume Distribution (VD):	0.465
Pgp-substrate:	5.298306465148926%

ADMET: Metabolism

CYP1A2-inhibitor:	0.017
CYP1A2-substrate:	0.896
CYP2C19-inhibitor:	0.191
CYP2C19-substrate:	0.593
CYP2C9-inhibitor:	0.101
CYP2C9-substrate:	0.834
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.78
CYP3A4-inhibitor:	0.523
CYP3A4-substrate:	0.023

ADMET: Excretion

Clearance (CL):	3.944
Half-life (T1/2):	0.851

ADMET: Toxicity

hERG Blockers:	0.402
Human Hepatotoxicity (H-HT):	0.268
Drug-inuced Liver Injury (DILI):	0.006
AMES Toxicity:	0.104
Rat Oral Acute Toxicity:	0.465
Maximum Recommended Daily Dose:	0.919
Skin Sensitization:	0.928
Carcinogencity:	0.143
Eye Corrosion:	0.062
Eye Irritation:	0.033
Respiratory Toxicity:	0.825

Download Data

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

Natural Product: NPC238646

Natural Product ID:	NPC238646
*Common Name:**	1-O-(15'-Methylhexadecyl)-Sn-Glycero-3-Phosphocholine
IUPAC Name:	[(2R)-2-hydroxy-3-(15-methylhexadecoxy)propyl] 2-(trimethylazaniumyl)ethyl phosphate
Synonyms:
Standard InCHIKey:	RQCNXHQIZGDHRA-RUZDIDTESA-N
Standard InCHI:	InChI=1S/C25H54NO6P/c1-24(2)18-16-14-12-10-8-6-7-9-11-13-15-17-20-30-22-25(27)23-32-33(28,29)31-21-19-26(3,4)5/h24-25,27H,6-23H2,1-5H3/t25-/m1/s1
SMILES:	O[C@@H](COP(=O)(OCC[N+](C)(C)C)[O-])COCCCCCCCCCCCCCCC(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL479688
PubChem CID:	10074520
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000256] Glycerophospholipids [CHEMONTID:0002213] Glycerophosphocholines [CHEMONTID:0001414] Monoalkylglycerophosphocholines

*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
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10579872]
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11325244]
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12088447]
NPO85	Spirastrella abata	Species	Spirastrellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[22182501]

☑ 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

Activity Type	# Activity
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	320.0	ug.mL-1	PMID[526236]

☑ 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 NPC238646 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	198
0.1-0.2	7912
0.2-0.3	20640
0.3-0.4	12388
0.4-0.5	1344
0.5-0.6	176
0.6-0.7	23
0.7-0.8	12
0.8-0.85	0
0.85-0.9	0
0.9-0.95	3
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9167	High Similarity	NPC474627
0.9167	High Similarity	NPC201338
0.9167	High Similarity	NPC328786
0.8219	Intermediate Similarity	NPC474702
0.8056	Intermediate Similarity	NPC330017
0.7857	Intermediate Similarity	NPC33267
0.7857	Intermediate Similarity	NPC169976
0.7857	Intermediate Similarity	NPC126366
0.7857	Intermediate Similarity	NPC324165
0.7857	Intermediate Similarity	NPC170963
0.7857	Intermediate Similarity	NPC114640
0.7639	Intermediate Similarity	NPC305223
0.7222	Intermediate Similarity	NPC127145
0.7222	Intermediate Similarity	NPC475930
0.7123	Intermediate Similarity	NPC474674
0.7083	Intermediate Similarity	NPC320663
0.7083	Intermediate Similarity	NPC224700
0.7027	Intermediate Similarity	NPC54460
0.6986	Remote Similarity	NPC137620
0.6986	Remote Similarity	NPC474675
0.6901	Remote Similarity	NPC474402
0.6885	Remote Similarity	NPC81384
0.6875	Remote Similarity	NPC473872
0.6707	Remote Similarity	NPC178758
0.6707	Remote Similarity	NPC196102
0.6667	Remote Similarity	NPC470268
0.6667	Remote Similarity	NPC319131
0.6486	Remote Similarity	NPC195165
0.6429	Remote Similarity	NPC174485
0.6377	Remote Similarity	NPC322148
0.6375	Remote Similarity	NPC325936
0.6364	Remote Similarity	NPC474403
0.6292	Remote Similarity	NPC329906
0.6234	Remote Similarity	NPC477200
0.6197	Remote Similarity	NPC470363
0.6027	Remote Similarity	NPC17455
0.6	Remote Similarity	NPC293551
0.6	Remote Similarity	NPC93630
0.5904	Remote Similarity	NPC473984
0.5902	Remote Similarity	NPC152008
0.5882	Remote Similarity	NPC82799
0.5882	Remote Similarity	NPC149908
0.5882	Remote Similarity	NPC45906
0.5882	Remote Similarity	NPC31313
0.5882	Remote Similarity	NPC288415
0.5882	Remote Similarity	NPC81006
0.5875	Remote Similarity	NPC43219
0.5867	Remote Similarity	NPC476702
0.5862	Remote Similarity	NPC476523
0.5833	Remote Similarity	NPC197039
0.5811	Remote Similarity	NPC145627
0.5802	Remote Similarity	NPC86064
0.5797	Remote Similarity	NPC270041
0.5781	Remote Similarity	NPC62014
0.5775	Remote Similarity	NPC8979
0.5733	Remote Similarity	NPC471419
0.5733	Remote Similarity	NPC163134
0.5714	Remote Similarity	NPC477756
0.5714	Remote Similarity	NPC477751
0.5714	Remote Similarity	NPC477752
0.5714	Remote Similarity	NPC477764
0.5652	Remote Similarity	NPC123814
0.5647	Remote Similarity	NPC90839
0.5641	Remote Similarity	NPC74555
0.5641	Remote Similarity	NPC477754
0.5641	Remote Similarity	NPC306763
0.5641	Remote Similarity	NPC266242
0.5641	Remote Similarity	NPC477759
0.5641	Remote Similarity	NPC254617
0.5641	Remote Similarity	NPC477760
0.5641	Remote Similarity	NPC477758
0.5641	Remote Similarity	NPC477761
0.5625	Remote Similarity	NPC476696
0.5625	Remote Similarity	NPC476695
0.5625	Remote Similarity	NPC476694
0.5625	Remote Similarity	NPC321873
0.5616	Remote Similarity	NPC471421
0.5616	Remote Similarity	NPC233364
0.5606	Remote Similarity	NPC8597
0.5606	Remote Similarity	NPC289484
0.5606	Remote Similarity	NPC319709
0.5604	Remote Similarity	NPC470284
0.56	Remote Similarity	NPC172622

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 NPC238646 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	203
0.1-0.2	3906
0.2-0.3	3676
0.3-0.4	1106
0.4-0.5	202
0.5-0.6	45
0.6-0.7	8
0.7-0.8	3
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
0.85	High Similarity	NPD6950	Discontinued
0.8154	Intermediate Similarity	NPD7347	Clinical (unspecified phase)
0.7333	Intermediate Similarity	NPD4840	Approved
0.7222	Intermediate Similarity	NPD8277	Approved
0.7083	Intermediate Similarity	NPD8278	Approved
0.6984	Remote Similarity	NPD7348	Clinical (unspecified phase)
0.6885	Remote Similarity	NPD9462	Approved
0.6885	Remote Similarity	NPD9463	Phase 3
0.6567	Remote Similarity	NPD6706	Discontinued
0.6471	Remote Similarity	NPD6439	Phase 3
0.625	Remote Similarity	NPD6949	Clinical (unspecified phase)
0.625	Remote Similarity	NPD4283	Discontinued
0.6234	Remote Similarity	NPD7535	Discontinued
0.5978	Remote Similarity	NPD6948	Phase 3
0.5949	Remote Similarity	NPD3187	Discontinued
0.5921	Remote Similarity	NPD5380	Approved
0.5902	Remote Similarity	NPD7536	Approved
0.5784	Remote Similarity	NPD3188	Approved
0.5658	Remote Similarity	NPD4272	Discontinued
0.5652	Remote Similarity	NPD3215	Phase 1
0.5606	Remote Similarity	NPD3211	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