NPASS Compound

Structure

NPC161344 OpenBabel07101719252D 29 29 0 0 1 0 0 0 0 0999 V2000 4.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4483 1.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5517 -1.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3912 -0.7934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9319 -0.5176 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6730 0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2247 -1.2247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5000 0.8660 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 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 4.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 1.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7071 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2588 -0.9659 0.0000 C 0 0 2 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 6.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 1 18 1 0 0 0 0 2 19 1 0 0 0 0 3 20 1 0 0 0 0 4 21 1 0 0 0 0 6 8 1 0 0 0 0 6 9 1 0 0 0 0 7 10 1 0 0 0 0 7 11 1 0 0 0 0 8 18 2 0 0 0 0 9 19 1 0 0 0 0 10 20 2 0 0 0 0 11 21 1 0 0 0 0 12 14 1 0 0 0 0 12 18 1 0 0 0 0 13 16 1 0 0 0 0 13 19 2 0 0 0 0 14 23 1 0 0 0 0 15 17 1 0 0 0 0 15 26 1 0 0 0 0 16 29 1 0 0 0 0 17 29 1 0 0 0 0 20 23 1 0 0 0 0 21 23 1 1 0 0 0 22 24 2 0 0 0 0 22 25 1 0 0 0 0 22 26 1 0 0 0 0 23 5 1 1 0 0 0 27 29 2 0 0 0 0 28 29 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	423.29
Volume:	456.342
LogP:	3.136
LogD:	3.251
LogS:	-3.221
# Rotatable Bonds:	11
TPSA:	98.54
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.29
Synthetic Accessibility Score:	4.329
Fsp3:	0.696
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.656
MDCK Permeability:	1.2429491107468493e-05
Pgp-inhibitor:	0.402
Pgp-substrate:	0.607
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.331
30% Bioavailability (F30%):	0.015

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.926
Plasma Protein Binding (PPB):	91.29285430908203%
Volume Distribution (VD):	1.18
Pgp-substrate:	14.85175895690918%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.086
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.144
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.016
CYP2D6-inhibitor:	0.955
CYP2D6-substrate:	0.124
CYP3A4-inhibitor:	0.569
CYP3A4-substrate:	0.213

ADMET: Excretion

Clearance (CL):	7.67
Half-life (T1/2):	0.092

ADMET: Toxicity

hERG Blockers:	0.401
Human Hepatotoxicity (H-HT):	0.615
Drug-inuced Liver Injury (DILI):	0.009
AMES Toxicity:	0.001
Rat Oral Acute Toxicity:	0.083
Maximum Recommended Daily Dose:	0.864
Skin Sensitization:	0.955
Carcinogencity:	0.017
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.246

Download Data

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

Natural Product: NPC161344

Natural Product ID:	NPC161344
*Common Name:**	Agelasidine C
IUPAC Name:	2-[2-[(2E,6E)-3,7-dimethyl-9-[(1S,6R)-1,2,6-trimethylcyclohex-2-en-1-yl]nona-2,6-dienyl]sulfonylethyl]guanidine
Synonyms:	Agelasidine C
Standard InCHIKey:	ZKAIIIOGWKNEAA-DEWOAGJPSA-N
Standard InCHI:	InChI=1S/C23H41N3O2S/c1-18(12-14-23(5)20(3)10-7-11-21(23)4)8-6-9-19(2)13-16-29(27,28)17-15-26-22(24)25/h8,10,13,21H,6-7,9,11-12,14-17H2,1-5H3,(H4,24,25,26)/b18-8+,19-13+/t21-,23-/m1/s1
SMILES:	NC(=N)NCCS(=O)(=O)C/C=C(/CC/C=C(/CC[C@@]1(C)[C@H](C)CCC=C1C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL598329
PubChem CID:	6438666
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] 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
NPO33334	agelas sponges	Species	Agelasidae	Eukaryota	n.a.	Indonesian	n.a.	PMID[20061160]

☑ 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
MIC	1
Others	1

Activity Type	# Activity
Cell Line	1
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1864	Cell Line	L5178Y	Mus musculus	GI	=	37.4	%	PMID[510832]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	5900.0	nM	PMID[510832]

☑ 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 NPC161344 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	192
0.1-0.2	14436
0.2-0.3	21885
0.3-0.4	5830
0.4-0.5	330
0.5-0.6	23
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.6146	Remote Similarity	NPC471867
0.5897	Remote Similarity	NPC153280
0.5882	Remote Similarity	NPC472544
0.5789	Remote Similarity	NPC57599
0.5729	Remote Similarity	NPC12035
0.5726	Remote Similarity	NPC477121
0.567	Remote Similarity	NPC329782
0.567	Remote Similarity	NPC118329
0.567	Remote Similarity	NPC152039
0.5647	Remote Similarity	NPC311809
0.5625	Remote Similarity	NPC211322
0.5612	Remote Similarity	NPC472312
0.5612	Remote Similarity	NPC471868
0.56	Remote Similarity	NPC24733

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 NPC161344 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	134
0.1-0.2	1680
0.2-0.3	5706
0.3-0.4	1507
0.4-0.5	121
0.5-0.6	2
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

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