NPASS Compound

Structure

NPC201338 OpenBabel07101719142D 32 31 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 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 -15.0000 -9.9282 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 -13.5000 -9.0622 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 -12.0000 -8.1962 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 -10.5000 -7.3301 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 -8.0000 -6.4641 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 -6.5000 -5.5981 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 -5.0000 -4.7321 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 -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 5 1 0 0 0 0 2 25 1 0 0 0 0 3 25 1 0 0 0 0 4 25 1 0 0 0 0 5 6 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 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 20 1 0 0 0 0 19 21 1 0 0 0 0 19 25 1 0 0 0 0 20 29 1 0 0 0 0 21 30 1 0 0 0 0 22 24 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 31 1 0 0 0 0 24 26 1 1 0 0 0 27 32 2 0 0 0 0 28 32 1 0 0 0 0 30 32 1 0 0 0 0 31 32 1 0 0 0 0 M CHG 2 25 1 28 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	481.35
Volume:	507.225
LogP:	2.365
LogD:	1.345
LogS:	0.036
# 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:	0.118
Synthetic Accessibility Score:	3.739
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:	-5.433
MDCK Permeability:	3.048217695322819e-05
Pgp-inhibitor:	0.015
Pgp-substrate:	0.595
Human Intestinal Absorption (HIA):	0.686
20% Bioavailability (F20%):	0.964
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	92.62129974365234%
Volume Distribution (VD):	0.45
Pgp-substrate:	8.280753135681152%

ADMET: Metabolism

CYP1A2-inhibitor:	0.016
CYP1A2-substrate:	0.902
CYP2C19-inhibitor:	0.2
CYP2C19-substrate:	0.45
CYP2C9-inhibitor:	0.052
CYP2C9-substrate:	0.746
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.85
CYP3A4-inhibitor:	0.471
CYP3A4-substrate:	0.019

ADMET: Excretion

Clearance (CL):	3.576
Half-life (T1/2):	0.852

ADMET: Toxicity

hERG Blockers:	0.443
Human Hepatotoxicity (H-HT):	0.256
Drug-inuced Liver Injury (DILI):	0.006
AMES Toxicity:	0.133
Rat Oral Acute Toxicity:	0.508
Maximum Recommended Daily Dose:	0.929
Skin Sensitization:	0.934
Carcinogencity:	0.155
Eye Corrosion:	0.072
Eye Irritation:	0.042
Respiratory Toxicity:	0.826

Download Data

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

Natural Product: NPC201338

Natural Product ID:	NPC201338
*Common Name:**	1-O-Hexadecyl-Sn-Glycero-3-Phosphocholine
IUPAC Name:	[(2R)-3-hexadecoxy-2-hydroxypropyl] 2-(trimethylazaniumyl)ethyl phosphate
Synonyms:
Standard InCHIKey:	VLBPIWYTPAXCFJ-XMMPIXPASA-N
Standard InCHI:	InChI=1S/C24H52NO6P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-20-29-22-24(26)23-31-32(27,28)30-21-19-25(2,3)4/h24,26H,5-23H2,1-4H3/t24-/m1/s1
SMILES:	CCCCCCCCCCCCCCCCOC[C@H](COP(=O)([O-])OCC[N+](C)(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL479687
PubChem CID:	162126
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
ED50	5
IC50	1

Activity Type	# Activity
Cell Line	5
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	5.5	ug ml-1	PMID[506179]
NPT146	Cell Line	SK-OV-3	Homo sapiens	ED50	=	4.9	ug ml-1	PMID[506179]
NPT2358	Cell Line	SK-MEL3	Homo sapiens	ED50	=	5.4	ug ml-1	PMID[506179]
NPT574	Cell Line	XF498	Homo sapiens	ED50	=	4.9	ug ml-1	PMID[506179]
NPT148	Cell Line	HCT-15	Homo sapiens	ED50	=	5.4	ug ml-1	PMID[506179]
NPT2	Others	Unspecified		IC50	=	422.0	ug.mL-1	PMID[506180]

☑ 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 NPC201338 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	411
0.1-0.2	15487
0.2-0.3	19701
0.3-0.4	6119
0.4-0.5	793
0.5-0.6	144
0.6-0.7	15
0.7-0.8	16
0.8-0.85	7
0.85-0.9	0
0.9-0.95	1
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC328786
1.0	High Similarity	NPC474627
0.9167	High Similarity	NPC238646
0.8462	Intermediate Similarity	NPC170963
0.8462	Intermediate Similarity	NPC324165
0.8462	Intermediate Similarity	NPC169976
0.8462	Intermediate Similarity	NPC114640
0.8462	Intermediate Similarity	NPC126366
0.8462	Intermediate Similarity	NPC33267
0.8209	Intermediate Similarity	NPC305223
0.7761	Intermediate Similarity	NPC127145
0.7761	Intermediate Similarity	NPC475930
0.7647	Intermediate Similarity	NPC474674
0.7612	Intermediate Similarity	NPC320663
0.7612	Intermediate Similarity	NPC224700
0.7536	Intermediate Similarity	NPC54460
0.7534	Intermediate Similarity	NPC474702
0.75	Intermediate Similarity	NPC474675
0.75	Intermediate Similarity	NPC137620
0.75	Intermediate Similarity	NPC81384
0.7458	Intermediate Similarity	NPC473872
0.7361	Intermediate Similarity	NPC330017
0.7188	Intermediate Similarity	NPC319131
0.7143	Intermediate Similarity	NPC196102
0.7143	Intermediate Similarity	NPC178758
0.6923	Remote Similarity	NPC174485
0.68	Remote Similarity	NPC325936
0.6471	Remote Similarity	NPC17455
0.6462	Remote Similarity	NPC293551
0.6429	Remote Similarity	NPC152008
0.6429	Remote Similarity	NPC474402
0.6364	Remote Similarity	NPC197039
0.6271	Remote Similarity	NPC62014
0.625	Remote Similarity	NPC82799
0.625	Remote Similarity	NPC270041
0.6232	Remote Similarity	NPC145627
0.6212	Remote Similarity	NPC8979
0.6143	Remote Similarity	NPC471419
0.6143	Remote Similarity	NPC163134
0.6094	Remote Similarity	NPC123814
0.6066	Remote Similarity	NPC319709
0.6066	Remote Similarity	NPC289484
0.6066	Remote Similarity	NPC8597
0.6029	Remote Similarity	NPC471421
0.6029	Remote Similarity	NPC233364
0.6027	Remote Similarity	NPC306763
0.6027	Remote Similarity	NPC74555
0.6027	Remote Similarity	NPC254617
0.6027	Remote Similarity	NPC266242
0.6	Remote Similarity	NPC470268
0.6	Remote Similarity	NPC321873
0.6	Remote Similarity	NPC476695
0.6	Remote Similarity	NPC476696
0.6	Remote Similarity	NPC476694
0.5972	Remote Similarity	NPC322319
0.5972	Remote Similarity	NPC326651
0.5972	Remote Similarity	NPC325117
0.5946	Remote Similarity	NPC473419
0.5946	Remote Similarity	NPC475127
0.5946	Remote Similarity	NPC475715
0.5926	Remote Similarity	NPC471420
0.5921	Remote Similarity	NPC474403
0.5909	Remote Similarity	NPC289979
0.5909	Remote Similarity	NPC23155
0.5909	Remote Similarity	NPC469937
0.5909	Remote Similarity	NPC53463
0.5909	Remote Similarity	NPC320588
0.589	Remote Similarity	NPC184150
0.589	Remote Similarity	NPC141156
0.589	Remote Similarity	NPC59221
0.5867	Remote Similarity	NPC163538
0.5867	Remote Similarity	NPC115800
0.5846	Remote Similarity	NPC474322
0.5811	Remote Similarity	NPC195165
0.5811	Remote Similarity	NPC474469
0.5811	Remote Similarity	NPC171850
0.5753	Remote Similarity	NPC12514
0.5753	Remote Similarity	NPC294883
0.5735	Remote Similarity	NPC471605
0.5735	Remote Similarity	NPC148424
0.5735	Remote Similarity	NPC471443
0.5733	Remote Similarity	NPC474299
0.5733	Remote Similarity	NPC474298
0.5733	Remote Similarity	NPC268922
0.5733	Remote Similarity	NPC473985
0.5733	Remote Similarity	NPC475808
0.5733	Remote Similarity	NPC28348
0.573	Remote Similarity	NPC329906
0.5714	Remote Similarity	NPC474914
0.5714	Remote Similarity	NPC474392
0.5714	Remote Similarity	NPC474468
0.5692	Remote Similarity	NPC329095
0.5679	Remote Similarity	NPC150557
0.5658	Remote Similarity	NPC473710
0.5658	Remote Similarity	NPC475694
0.5652	Remote Similarity	NPC322148
0.5616	Remote Similarity	NPC233034
0.5606	Remote Similarity	NPC320043
0.5606	Remote Similarity	NPC103672
0.56	Remote Similarity	NPC34291
0.56	Remote Similarity	NPC471418
0.56	Remote Similarity	NPC126664

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 NPC201338 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	351
0.1-0.2	4809
0.2-0.3	2996
0.3-0.4	740
0.4-0.5	204
0.5-0.6	37
0.6-0.7	6
0.7-0.8	6
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9273	High Similarity	NPD6950	Discontinued
0.8	Intermediate Similarity	NPD4840	Approved
0.7937	Intermediate Similarity	NPD7347	Clinical (unspecified phase)
0.7761	Intermediate Similarity	NPD8277	Approved
0.7612	Intermediate Similarity	NPD8278	Approved
0.75	Intermediate Similarity	NPD9463	Phase 3
0.75	Intermediate Similarity	NPD9462	Approved
0.7097	Intermediate Similarity	NPD6706	Discontinued
0.6984	Remote Similarity	NPD6439	Phase 3
0.6716	Remote Similarity	NPD4283	Discontinued
0.6716	Remote Similarity	NPD6949	Clinical (unspecified phase)
0.6429	Remote Similarity	NPD7536	Approved
0.6338	Remote Similarity	NPD5380	Approved
0.6322	Remote Similarity	NPD6948	Phase 3
0.619	Remote Similarity	NPD7348	Clinical (unspecified phase)
0.6094	Remote Similarity	NPD3215	Phase 1
0.6066	Remote Similarity	NPD3211	Approved
0.6	Remote Similarity	NPD7535	Discontinued
0.5965	Remote Similarity	NPD5799	Discontinued
0.5909	Remote Similarity	NPD3728	Approved
0.5909	Remote Similarity	NPD3730	Approved
0.5857	Remote Similarity	NPD393	Approved
0.5833	Remote Similarity	NPD1457	Discontinued
0.5781	Remote Similarity	NPD3214	Discontinued
0.5761	Remote Similarity	NPD5789	Clinical (unspecified phase)
0.5729	Remote Similarity	NPD6946	Approved
0.5714	Remote Similarity	NPD9455	Approved
0.5645	Remote Similarity	NPD1152	Phase 2
0.5641	Remote Similarity	NPD389	Phase 3
0.5616	Remote Similarity	NPD9440	Discontinued
0.5606	Remote Similarity	NPD9049	Discontinued
0.5606	Remote Similarity	NPD9050	Approved
0.56	Remote Similarity	NPD9443	Clinical (unspecified phase)
0.56	Remote Similarity	NPD9444	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