NPASS Compound

Structure

NPC480902 OpenBabel06302216182D 26 27 0 0 1 0 0 0 0 0999 V2000 3.8634 -5.0979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6412 -4.1229 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.6662 -3.9001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2326 -2.9990 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 2.6668 -2.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6418 -1.8759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4235 -2.4996 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.2896 -1.9996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2899 -0.9999 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1560 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0222 -1.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0219 -2.0001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8878 -2.5006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8875 -3.5006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0213 -4.0002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1552 -3.5001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2890 -3.9997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4232 -3.4996 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.3667 -2.4987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3670 -1.4988 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3664 -3.4987 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.5006 -2.9985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3662 -4.4987 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -4.9985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2320 -4.9990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0982 -4.4992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 18 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 19 1 0 0 0 0 4 21 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 7 18 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 19 20 2 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 M CHG 1 4 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	366.3
Volume:	405.368
LogP:	2.269
LogD:	3.948
LogS:	-1.184
# Rotatable Bonds:	4
TPSA:	43.37
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.413
Synthetic Accessibility Score:	4.767
Fsp3:	0.909
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.266
MDCK Permeability:	5.437863728730008e-05
Pgp-inhibitor:	0.001
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.973
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.071
Plasma Protein Binding (PPB):	55.41795349121094%
Volume Distribution (VD):	0.895
Pgp-substrate:	19.636648178100586%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.238
CYP2C19-inhibitor:	0.112
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.098
CYP2D6-inhibitor:	0.487
CYP2D6-substrate:	0.2
CYP3A4-inhibitor:	0.287
CYP3A4-substrate:	0.311

ADMET: Excretion

Clearance (CL):	3.994
Half-life (T1/2):	0.905

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.042
Drug-inuced Liver Injury (DILI):	0.075
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.965
Skin Sensitization:	0.97
Carcinogencity:	0.065
Eye Corrosion:	0.944
Eye Irritation:	0.679
Respiratory Toxicity:	0.542

Download Data

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

Natural Product: NPC480902

Natural Product ID:	NPC480902
*Common Name:**	WKOUDHUKUOPVHB-IFTCTDCCSA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WKOUDHUKUOPVHB-IFTCTDCCSA-M
Standard InCHI:	InChI=1S/C22H40NO3.ClH/c1-18-16-23(17-24,19(2)22(25)26-3)15-14-20-12-10-8-6-4-5-7-9-11-13-21(18)20;/h17-21H,4-16H2,1-3H3;1H/q+1;/p-1/t18-,19-,20+,21-,23-;/m0./s1
SMILES:	C[C@H]1C[N@@+](CC[C@H]2CCCCCCCCCC[C@@H]12)(C=O)[C@@H](C)C(=O)OC.[Cl-]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds]

*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
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	red sea	n.a.	PMID[12762806]
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[18027906]
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[22469701]
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	collected by hand at a depth of 10 m off the shore of Iriomote Island, Okinawa Prefecture, Japan	2009-JUN	PMID[23855338]
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[24948562]
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[27015002]
NPO33070	Callyspongia sp.	Species	n.a.	n.a.	n.a.	New Guinea	n.a.	PMID[8158156]

☑ 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	2
MIC	6

Activity Type	# Activity
Cell Line	2
Organism	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	=	3000.0	nM	PMID[27015002]
NPT111	Cell Line	K562	Homo sapiens	IC50	=	7400.0	nM	PMID[27015002]
NPT22	Organism	Bacillus subtilis subsp. spizizenii	Bacillus subtilis subsp. spizizenii	MIC	>=	128000.0	nM	PMID[27015002]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>=	128000.0	nM	PMID[27015002]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	>=	128000.0	nM	PMID[27015002]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	>=	128000.0	nM	PMID[27015002]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	>=	128000.0	nM	PMID[27015002]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>=	128000.0	nM	PMID[27015002]

☑ 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 NPC480902 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	209
0.1-0.2	18334
0.2-0.3	19713
0.3-0.4	3721
0.4-0.5	635
0.5-0.6	72
0.6-0.7	12
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

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 NPC480902 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	123
0.1-0.2	3457
0.2-0.3	4290
0.3-0.4	1039
0.4-0.5	213
0.5-0.6	25
0.6-0.7	3
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

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