NPASS Compound

Structure

CID291196 OpenBabel06191716102D 38 37 0 0 1 0 0 0 0 0999 V2000 8.6603 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -8.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 4.0000 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 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 2 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 0.8660 1.5000 0.0000 N 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 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 1 0 0 0 0 2 4 1 0 0 0 0 3 5 1 0 0 0 0 4 6 1 0 0 0 0 5 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 19 1 0 0 0 0 18 20 1 0 0 0 0 19 21 1 0 0 0 0 20 22 1 0 0 0 0 21 23 1 0 0 0 0 22 24 1 0 0 0 0 23 25 1 0 0 0 0 24 26 1 0 0 0 0 25 27 1 0 0 0 0 26 28 1 0 0 0 0 27 29 2 0 0 0 0 28 30 1 0 0 0 0 29 33 1 0 0 0 0 30 34 1 0 0 0 0 31 36 1 0 0 0 0 32 31 1 1 0 0 0 32 33 1 0 0 0 0 32 35 1 0 0 0 0 33 37 1 1 0 0 0 34 35 2 3 0 0 0 34 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	537.51
Volume:	628.714
LogP:	10.592
LogD:	4.982
LogS:	-3.871
# Rotatable Bonds:	31
TPSA:	69.56
# H-Bond Aceptor:	4
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.063
Synthetic Accessibility Score:	3.269
Fsp3:	0.912
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.252
MDCK Permeability:	7.197513696155511e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.611
Human Intestinal Absorption (HIA):	0.035
20% Bioavailability (F20%):	0.751
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	98.8884506225586%
Volume Distribution (VD):	1.519
Pgp-substrate:	1.3993765115737915%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.157
CYP2C19-inhibitor:	0.132
CYP2C19-substrate:	0.04
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.987
CYP2D6-inhibitor:	0.418
CYP2D6-substrate:	0.031
CYP3A4-inhibitor:	0.266
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	3.47
Half-life (T1/2):	0.101

ADMET: Toxicity

hERG Blockers:	0.406
Human Hepatotoxicity (H-HT):	0.117
Drug-inuced Liver Injury (DILI):	0.023
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.047
Skin Sensitization:	0.965
Carcinogencity:	0.009
Eye Corrosion:	0.005
Eye Irritation:	0.224
Respiratory Toxicity:	0.613

Download Data

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

Natural Product: NPC291196

Natural Product ID:	NPC291196
*Common Name:**	N-[(E,2S,3R)-1,3-Dihydroxyoctadec-4-En-2-Yl]Hexadecanamide
IUPAC Name:	N-[(E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl]hexadecanamide
Synonyms:	N-Palmitoylsphingosine
Standard InCHIKey:	YDNKGFDKKRUKPY-TURZORIXSA-N
Standard InCHI:	InChI=1S/C34H67NO3/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-33(37)32(31-36)35-34(38)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2/h27,29,32-33,36-37H,3-26,28,30-31H2,1-2H3,(H,35,38)/b29-27+/t32-,33+/m0/s1
SMILES:	CCCCCCCCCCCCCCCC(=N[C@H]([C@@H](/C=C/CCCCCCCCCCCCC)O)CO)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL35292
PubChem CID:	5283564
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000257] Sphingolipids [CHEMONTID:0001418] Ceramides [CHEMONTID:0001669] Long-chain ceramides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9949311]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9892086]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9870205]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9869364]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9869358]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	blood	n.a.	PMID[9861496]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9861478]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9857238]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	urine	n.a.	PMID[9851755]
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	n.a.	cerebrospinal fluid	n.a.	PMID[9818465]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
Others	1
Potency	2

Activity Type	# Activity
Individual Protein	3
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT24905	SINGLE PROTEIN	Collagen type IV alpha-3-binding protein	Homo sapiens	Inhibition	=	25.0	%	PMID[469831]
NPT443	Individual Protein	Histone acetyltransferase GCN5	Homo sapiens	Potency	n.a.	141.3	nM	PMID[469830]
NPT698	Individual Protein	Regulator of G-protein signaling 4	Homo sapiens	Potency	n.a.	211.9	nM	PMID[469830]
NPT910	Individual Protein	Cholesteryl ester transfer protein	Homo sapiens	IC50	=	65600.0	nM	PMID[469828]

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☑ 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 NPC291196 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	49
0.1-0.2	721
0.2-0.3	21272
0.3-0.4	14625
0.4-0.5	4779
0.5-0.6	964
0.6-0.7	209
0.7-0.8	62
0.8-0.85	7
0.85-0.9	3
0.9-0.95	2
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC103712
0.9412	High Similarity	NPC288086
0.8594	High Similarity	NPC329003
0.8594	High Similarity	NPC326524
0.8594	High Similarity	NPC325550

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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 NPC291196 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	57
0.1-0.2	735
0.2-0.3	5281
0.3-0.4	2569
0.4-0.5	437
0.5-0.6	63
0.6-0.7	5
0.7-0.8	3
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7941	Intermediate Similarity	NPD3210	Clinical (unspecified phase)
0.7619	Intermediate Similarity	NPD8522	Clinical (unspecified phase)
0.72	Intermediate Similarity	NPD3212	Clinical (unspecified phase)
0.6719	Remote Similarity	NPD3211	Approved
0.6351	Remote Similarity	NPD6949	Clinical (unspecified phase)

Showing 1 to 5 of 33 entries

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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