NPASS Compound

Structure

NPC474126 OpenBabel07101718182D 30 29 0 0 1 0 0 0 0 0999 V2000 13.0000 -5.8301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.5000 -4.9641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0000 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 -0.6340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.0000 -4.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0000 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.0000 -4.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0000 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5000 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.5000 -3.2321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0000 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0000 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0000 -4.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.5000 -4.9641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5000 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.5000 -1.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 10.5000 -3.2321 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.5000 -0.5000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3660 -2.7321 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 8.0000 -2.3660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6340 -3.7321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 -4.0981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 -1.5000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 8.5000 -3.2321 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 4 19 1 0 0 0 0 5 8 1 0 0 0 0 5 12 1 0 0 0 0 6 9 1 0 0 0 0 6 10 1 0 0 0 0 7 11 1 0 0 0 0 7 13 1 0 0 0 0 8 17 1 0 0 0 0 9 18 1 0 0 0 0 10 19 1 0 0 0 0 11 18 1 0 0 0 0 12 20 1 0 0 0 0 13 20 1 0 0 0 0 14 15 1 0 0 0 0 14 19 1 0 0 0 0 15 27 1 0 0 0 0 16 20 1 0 0 0 0 16 28 1 0 0 0 0 21 29 1 0 0 0 0 22 29 2 0 0 0 0 23 29 2 0 0 0 0 24 30 1 0 0 0 0 25 30 2 0 0 0 0 26 30 2 0 0 0 0 27 29 1 0 0 0 0 28 30 1 0 0 0 0 M CHG 2 21 -1 24 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	472.22
Volume:	459.18
LogP:	3.778
LogD:	2.162
LogS:	-5.062
# Rotatable Bonds:	19
TPSA:	132.86
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.2
Synthetic Accessibility Score:	4.346
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:	-4.775
MDCK Permeability:	4.008435280411504e-05
Pgp-inhibitor:	0.176
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.052
Plasma Protein Binding (PPB):	99.8871078491211%
Volume Distribution (VD):	1.314
Pgp-substrate:	0.9738819599151611%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.467
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.9
CYP2C9-inhibitor:	0.18
CYP2C9-substrate:	0.928
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.077
CYP3A4-inhibitor:	0.007
CYP3A4-substrate:	0.021

ADMET: Excretion

Clearance (CL):	1.766
Half-life (T1/2):	0.006

ADMET: Toxicity

hERG Blockers:	0.217
Human Hepatotoxicity (H-HT):	0.937
Drug-inuced Liver Injury (DILI):	0.191
AMES Toxicity:	0.974
Rat Oral Acute Toxicity:	0.026
Maximum Recommended Daily Dose:	0.888
Skin Sensitization:	0.983
Carcinogencity:	0.926
Eye Corrosion:	0.992
Eye Irritation:	0.926
Respiratory Toxicity:	0.99

Download Data

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

Natural Product: NPC474126

Natural Product ID:	NPC474126
*Common Name:**	Sodium 3,7,11,15-Tetramethylhexadeca-1,19-Diyl Sulfate
IUPAC Name:	disodium;[6,10-dimethyl-2-(4-methylpentyl)-12-sulfonatooxydodecyl] sulfate
Synonyms:
Standard InCHIKey:	DSFXFAVFISJFNZ-UHFFFAOYSA-L
Standard InCHI:	InChI=1S/C20H42O8S2.2Na/c1-17(2)8-5-12-20(16-28-30(24,25)26)13-7-11-18(3)9-6-10-19(4)14-15-27-29(21,22)23;;/h17-20H,5-16H2,1-4H3,(H,21,22,23)(H,24,25,26);;/q;2*+1/p-2
SMILES:	CC(CCCC(COS(=O)(=O)[O-])CCCC(C)C)CCCC(CCOS(=O)(=O)[O-])C.[Na+].[Na+]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL462531
PubChem CID:	10481736
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001357] Acyclic diterpenoids

*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
NPO23405	Sidnyum turbinatum	n.a.	n.a.	n.a.	n.a.	Mediterranean	n.a.	PMID[11430005]
NPO23405	Sidnyum turbinatum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3470	Cell Line	WEHI-164	Mus musculus	IC50	=	300.0	ug.mL-1	PMID[513567]

☑ 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 NPC474126 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	741
0.1-0.2	17565
0.2-0.3	15489
0.3-0.4	8161
0.4-0.5	644
0.5-0.6	82
0.6-0.7	7
0.7-0.8	6
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC474125
0.8049	Intermediate Similarity	NPC473568
0.8049	Intermediate Similarity	NPC469714
0.8049	Intermediate Similarity	NPC469712
0.7949	Intermediate Similarity	NPC474089
0.7949	Intermediate Similarity	NPC474120
0.7442	Intermediate Similarity	NPC221022
0.7436	Intermediate Similarity	NPC272426
0.6977	Remote Similarity	NPC177022
0.6889	Remote Similarity	NPC160261
0.6889	Remote Similarity	NPC469759
0.6531	Remote Similarity	NPC473914
0.65	Remote Similarity	NPC477603
0.64	Remote Similarity	NPC249754
0.6327	Remote Similarity	NPC215358
0.629	Remote Similarity	NPC475172
0.6279	Remote Similarity	NPC283682
0.62	Remote Similarity	NPC308301
0.617	Remote Similarity	NPC152008
0.6154	Remote Similarity	NPC474048
0.6087	Remote Similarity	NPC316546
0.6047	Remote Similarity	NPC185538
0.6047	Remote Similarity	NPC291158
0.6047	Remote Similarity	NPC181516
0.6047	Remote Similarity	NPC152759
0.6047	Remote Similarity	NPC205141
0.6047	Remote Similarity	NPC12231
0.6047	Remote Similarity	NPC139131
0.6047	Remote Similarity	NPC272998
0.6	Remote Similarity	NPC474914
0.6	Remote Similarity	NPC328441
0.6	Remote Similarity	NPC474392
0.5962	Remote Similarity	NPC477878
0.5962	Remote Similarity	NPC13105
0.5962	Remote Similarity	NPC324793
0.5909	Remote Similarity	NPC478103
0.5909	Remote Similarity	NPC139569
0.5909	Remote Similarity	NPC324984
0.5909	Remote Similarity	NPC477823
0.5909	Remote Similarity	NPC477821
0.5909	Remote Similarity	NPC473552
0.5909	Remote Similarity	NPC477822
0.5909	Remote Similarity	NPC323900
0.5897	Remote Similarity	NPC172053
0.5882	Remote Similarity	NPC87439
0.587	Remote Similarity	NPC74352
0.587	Remote Similarity	NPC128996
0.5862	Remote Similarity	NPC322148
0.5814	Remote Similarity	NPC126915
0.58	Remote Similarity	NPC144891
0.5778	Remote Similarity	NPC97967
0.5769	Remote Similarity	NPC176309
0.5769	Remote Similarity	NPC21844
0.5769	Remote Similarity	NPC198540
0.5769	Remote Similarity	NPC223468
0.5769	Remote Similarity	NPC147343
0.5769	Remote Similarity	NPC287550
0.5769	Remote Similarity	NPC84030
0.5745	Remote Similarity	NPC197039
0.5741	Remote Similarity	NPC305182
0.5741	Remote Similarity	NPC142103
0.5735	Remote Similarity	NPC478130
0.5714	Remote Similarity	NPC72722
0.5667	Remote Similarity	NPC226602
0.5667	Remote Similarity	NPC125506
0.5667	Remote Similarity	NPC472019
0.5667	Remote Similarity	NPC472020
0.5652	Remote Similarity	NPC61665
0.5652	Remote Similarity	NPC478105
0.5636	Remote Similarity	NPC274261
0.5636	Remote Similarity	NPC307022
0.5636	Remote Similarity	NPC291724

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 NPC474126 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1006
0.1-0.2	5830
0.2-0.3	1830
0.3-0.4	414
0.4-0.5	46
0.5-0.6	19
0.6-0.7	0
0.7-0.8	4
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
0.8537	High Similarity	NPD1460	Approved
0.814	Intermediate Similarity	NPD1462	Approved
0.7436	Intermediate Similarity	NPD1461	Approved
0.7436	Intermediate Similarity	NPD908	Approved
0.7436	Intermediate Similarity	NPD907	Approved
0.6226	Remote Similarity	NPD7348	Clinical (unspecified phase)
0.617	Remote Similarity	NPD7536	Approved
0.6047	Remote Similarity	NPD2272	Approved
0.6047	Remote Similarity	NPD5383	Approved
0.5957	Remote Similarity	NPD5799	Discontinued
0.5862	Remote Similarity	NPD4279	Approved
0.5769	Remote Similarity	NPD384	Approved
0.5769	Remote Similarity	NPD385	Approved
0.5714	Remote Similarity	NPD9426	Discontinued
0.5667	Remote Similarity	NPD4280	Approved
0.5614	Remote Similarity	NPD3729	Clinical (unspecified phase)

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