NPASS Compound

Structure

NPC478615 OpenBabel06302215272D 28 30 0 0 1 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8680 0.5012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8680 1.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8680 1.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7361 2.0046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6041 1.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4721 2.0046 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6041 0.5012 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8680 -1.5035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8680 -2.5058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8680 -2.5058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8680 -1.5035 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7361 -1.0023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6041 -1.5035 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3871 2.0204 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.3200 2.7275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0612 3.6935 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.7427 3.3333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8860 2.5759 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.1697 3.6316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6118 3.2452 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.9047 3.9523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3530 2.2792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3832 1.9916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7361 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 10 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 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 2 3 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 18 1 0 0 0 0 18 27 1 0 0 0 0 18 19 1 0 0 0 0 18 26 1 0 0 0 0 19 20 1 0 0 0 0 20 25 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 22 27 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.3
Volume:	423.786
LogP:	5.504
LogD:	3.569
LogS:	-4.224
# Rotatable Bonds:	15
TPSA:	78.43
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.375
Synthetic Accessibility Score:	3.488
Fsp3:	0.913
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:	-5.121
MDCK Permeability:	3.3499494747957215e-05
Pgp-inhibitor:	0.011
Pgp-substrate:	0.11
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.058

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.078
Plasma Protein Binding (PPB):	92.22193145751953%
Volume Distribution (VD):	0.641
Pgp-substrate:	1.4502216577529907%

ADMET: Metabolism

CYP1A2-inhibitor:	0.063
CYP1A2-substrate:	0.133
CYP2C19-inhibitor:	0.519
CYP2C19-substrate:	0.081
CYP2C9-inhibitor:	0.474
CYP2C9-substrate:	0.995
CYP2D6-inhibitor:	0.491
CYP2D6-substrate:	0.135
CYP3A4-inhibitor:	0.141
CYP3A4-substrate:	0.012

ADMET: Excretion

Clearance (CL):	1.635
Half-life (T1/2):	0.194

ADMET: Toxicity

hERG Blockers:	0.008
Human Hepatotoxicity (H-HT):	0.53
Drug-inuced Liver Injury (DILI):	0.026
AMES Toxicity:	0.003
Rat Oral Acute Toxicity:	0.003
Maximum Recommended Daily Dose:	0.103
Skin Sensitization:	0.246
Carcinogencity:	0.059
Eye Corrosion:	0.003
Eye Irritation:	0.111
Respiratory Toxicity:	0.222

Download Data

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

Natural Product: NPC478615

Natural Product ID:	NPC478615
*Common Name:**	XLGSEOAVLVTJDH-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XLGSEOAVLVTJDH-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H40N2O3/c26-21(27)10-8-6-4-2-1-3-5-7-9-11-24-22(28)25-23-15-18-12-19(16-23)14-20(13-18)17-23/h18-20H,1-17H2,(H,26,27)(H2,24,25,28)
SMILES:	C(CCCCCC(=O)O)CCCCCN=C(NC12CC3CC(CC(C3)C2)C1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10069117
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0003086] Medium-chain fatty acids

*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
NPO40918	Rubia philippinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27704813]
NPO15373	Actaea dahurica	Species	Ranunculaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28558206]
NPO40918	Rubia philippinensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30354105]
NPO15373	Actaea dahurica	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32031796]
NPO15373	Actaea dahurica	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15373	Actaea dahurica	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15373	Actaea dahurica	Species	Ranunculaceae	Eukaryota	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	40
Others	4

Activity Type	# Activity
Individual Protein	35
Others	4
SINGLE PROTEIN	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT166	Individual Protein	Acyl coenzyme A:cholesterol acyltransferase	Homo sapiens	Activity	=	100.0	%	PMID[17046265]
NPT203	Individual Protein	Carboxylesterase 2	Homo sapiens	Activity	=	100.0	%	PMID[17046265]
NPT5882	Individual Protein	Epoxide hydrolase 2	Rattus norvegicus	IC50	=	11.0	nM	PMID[17616115]
NPT5882	Individual Protein	Epoxide hydrolase 2	Rattus norvegicus	IC50	=	5.0	nM	PMID[19645482]
NPT5882	Individual Protein	Epoxide hydrolase 2	Rattus norvegicus	IC50	=	11.0	nM	PMID[21354674]
NPT570	Individual Protein	Arachidonate 5-lipoxygenase	Homo sapiens	IC50	=	107.0	nM	PMID[23356879]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[16870439]
NPT21303	SINGLE PROTEIN	Epoxide hydratase	Mus musculus	IC50	=	50.0	nM	PMID[16908134]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	100.0	nM	PMID[16908134]
NPT21303	SINGLE PROTEIN	Epoxide hydratase	Mus musculus	IC50	=	50.0	nM	PMID[17046265]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	100.0	nM	PMID[17046265]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.2	nM	PMID[17046265]
NPT21303	SINGLE PROTEIN	Epoxide hydratase	Mus musculus	IC50	=	10.0	nM	PMID[17616115]
NPT2	Others	Unspecified		IC50	=	5.0	nM	PMID[17616115]
NPT2	Others	Unspecified		IC50	=	3.0	nM	PMID[17616115]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[17616115]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[19653681]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	1.6	nM	PMID[19645482]
NPT21303	SINGLE PROTEIN	Epoxide hydratase	Mus musculus	IC50	=	7.0	nM	PMID[19645482]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[21070033]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[22079754]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	107.0	nM	PMID[23017883]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[21354674]
NPT21303	SINGLE PROTEIN	Epoxide hydratase	Mus musculus	IC50	=	10.0	nM	PMID[21354674]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	107.0	nM	PMID[23130964]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	68.0	nM	PMID[23489630]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	6.5	nM	DOI[10.1007/s00044-013-0817-8]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	10.3	nM	PMID[24679441]
NPT2	Others	Unspecified		IC50	=	13.0	nM	PMID[25479771]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	3.0	nM	PMID[25119815]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	10.9	nM	PMID[26372074]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	Inhibition	=	64.7	%	PMID[26483136]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	10.0	nM	PMID[26483136]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	107000.0	nM	PMID[26595749]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	59.0	nM	PMID[27092411]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	16.0	nM	PMID[27120257]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	0.35	nM	DOI[10.1039/C6MD00395H]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	7.8	nM	PMID[28558206]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	0.6	nM	PMID[30354105]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	4400.0	nM	PMID[31009908]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	69.0	nM	PMID[31009912]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	Inhibition	=	98.4	%	PMID[31693857]
NPT862	Individual Protein	Epoxide hydratase	Homo sapiens	IC50	=	490.0	nM	PMID[32763463]

☑ 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 NPC478615 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	135
0.1-0.2	4602
0.2-0.3	22538
0.3-0.4	11581
0.4-0.5	3437
0.5-0.6	393
0.6-0.7	10
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 NPC478615 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	79
0.1-0.2	1191
0.2-0.3	5498
0.3-0.4	1996
0.4-0.5	309
0.5-0.6	71
0.6-0.7	5
0.7-0.8	1
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