NPASS Compound

Structure

CID288086 OpenBabel06191716092D 47 46 0 0 1 0 0 0 0 0999 V2000 12.1244 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8564 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -15.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -14.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -12.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -11.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -9.5000 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 6.9282 -8.0000 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 6.0622 -6.5000 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 -6.9282 -2.0000 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 -6.0622 -1.5000 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 -2.0000 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 -1.5000 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 -3.4641 -2.0000 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 -2.5981 -1.5000 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 -1.7321 -2.0000 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 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 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 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 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 24 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 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 1 0 0 0 0 28 30 1 0 0 0 0 29 31 1 0 0 0 0 30 32 1 0 0 0 0 31 33 1 0 0 0 0 32 34 1 0 0 0 0 33 35 1 0 0 0 0 34 36 2 0 0 0 0 35 37 1 0 0 0 0 36 40 1 0 0 0 0 37 41 1 0 0 0 0 38 44 1 0 0 0 0 39 38 1 1 0 0 0 39 40 1 0 0 0 0 39 43 1 0 0 0 0 40 45 1 1 0 0 0 41 42 1 0 0 0 0 41 46 1 6 0 0 0 42 43 2 3 0 0 0 42 47 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	665.63
Volume:	775.873
LogP:	13.23
LogD:	5.315
LogS:	-2.879
# Rotatable Bonds:	39
TPSA:	89.79
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	0
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.039
Synthetic Accessibility Score:	3.669
Fsp3:	0.929
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:	-5.463
MDCK Permeability:	1.8003572677116608e-06
Pgp-inhibitor:	0.0
Pgp-substrate:	0.668
Human Intestinal Absorption (HIA):	0.079
20% Bioavailability (F20%):	0.944
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	102.64429473876953%
Volume Distribution (VD):	1.047
Pgp-substrate:	0.9096592664718628%

ADMET: Metabolism

CYP1A2-inhibitor:	0.021
CYP1A2-substrate:	0.126
CYP2C19-inhibitor:	0.094
CYP2C19-substrate:	0.034
CYP2C9-inhibitor:	0.019
CYP2C9-substrate:	0.995
CYP2D6-inhibitor:	0.301
CYP2D6-substrate:	0.024
CYP3A4-inhibitor:	0.163
CYP3A4-substrate:	0.005

ADMET: Excretion

Clearance (CL):	3.224
Half-life (T1/2):	0.039

ADMET: Toxicity

hERG Blockers:	0.655
Human Hepatotoxicity (H-HT):	0.085
Drug-inuced Liver Injury (DILI):	0.02
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.046
Maximum Recommended Daily Dose:	0.045
Skin Sensitization:	0.969
Carcinogencity:	0.004
Eye Corrosion:	0.003
Eye Irritation:	0.063
Respiratory Toxicity:	0.644

Download Data

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

Natural Product: NPC288086

Natural Product ID:	NPC288086
*Common Name:**	(2S,3R,4E)-2-N-(2'-Hydroxytetracosanoyl)-Heptadecasphinga-4-Ene
IUPAC Name:	(2R)-N-[(E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl]-2-hydroxytetracosanamide
Synonyms:
Standard InCHIKey:	WAYLDHLWVYQNSQ-CFBMXOPXSA-N
Standard InCHI:	InChI=1S/C42H83NO4/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-25-27-29-31-33-35-37-41(46)42(47)43-39(38-44)40(45)36-34-32-30-28-26-24-16-14-12-10-8-6-4-2/h34,36,39-41,44-46H,3-33,35,37-38H2,1-2H3,(H,43,47)/b36-34+/t39-,40+,41+/m0/s1
SMILES:	CCCCCCCCCCCCCCCCCCCCCC[C@H](C(=N[C@H]([C@@H](/C=C/CCCCCCCCCCCCC)O)CO)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2268779
PubChem CID:	76308629
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000257] Sphingolipids [CHEMONTID:0001418] 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
NPO9173	Munronia henryi	Species	Meliaceae	Eukaryota	whole plants	Wenshan, Yunnan Province, China	2012-Nov	PMID[25798528]
NPO3216	Comactinia meridionalis	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27626	Limonia acidissima	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9173	Munronia henryi	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 4 of 4 entries

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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
Others	2

Activity Type	# Activity
Organism	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT785	Organism	Pieris brassicae	Pieris brassicae	mortality	=	0.0	%	PMID[533598]
NPT785	Organism	Pieris brassicae	Pieris brassicae	Activity	=	0.0	%	PMID[533598]

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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 NPC288086 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	55
0.1-0.2	756
0.2-0.3	19428
0.3-0.4	16020
0.4-0.5	5198
0.5-0.6	1003
0.6-0.7	150
0.7-0.8	77
0.8-0.85	2
0.85-0.9	3
0.9-0.95	4
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9412	High Similarity	NPC103712
0.9412	High Similarity	NPC291196
0.9028	High Similarity	NPC217095
0.9028	High Similarity	NPC264417
0.8333	Intermediate Similarity	NPC82799

Showing 1 to 5 of 200 entries

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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 NPC288086 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	61
0.1-0.2	808
0.2-0.3	5149
0.3-0.4	2607
0.4-0.5	457
0.5-0.6	61
0.6-0.7	5
0.7-0.8	2
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
0.7882	Intermediate Similarity	NPD8522	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD3210	Clinical (unspecified phase)
0.7051	Intermediate Similarity	NPD3212	Clinical (unspecified phase)
0.6408	Remote Similarity	NPD6421	Discontinued
0.6341	Remote Similarity	NPD3187	Discontinued

Showing 1 to 5 of 26 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