NPASS Compound

Structure

NPC2354 OpenBabel06302216032D 22 21 0 0 1 0 0 0 0 0999 V2000 11.2583 0.5000 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 10.3923 2.0000 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 2.0000 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 6.9282 2.0000 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 5.1962 2.0000 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 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 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 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 0.8660 3.5000 0.0000 O 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 2.0000 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 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 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 2 0 0 0 0 13 14 1 0 0 0 0 13 19 1 0 0 0 0 14 15 1 0 0 0 0 14 18 1 6 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	310.21
Volume:	344.499
LogP:	4.387
LogD:	3.243
LogS:	-4.389
# Rotatable Bonds:	15
TPSA:	60.44
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	0
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.16
Synthetic Accessibility Score:	2.938
Fsp3:	0.722
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.688
MDCK Permeability:	2.6623627491062507e-05
Pgp-inhibitor:	0.964
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.927
30% Bioavailability (F30%):	0.928

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.972
Plasma Protein Binding (PPB):	90.22374725341797%
Volume Distribution (VD):	0.521
Pgp-substrate:	4.84437370300293%

ADMET: Metabolism

CYP1A2-inhibitor:	0.786
CYP1A2-substrate:	0.801
CYP2C19-inhibitor:	0.759
CYP2C19-substrate:	0.622
CYP2C9-inhibitor:	0.693
CYP2C9-substrate:	0.895
CYP2D6-inhibitor:	0.04
CYP2D6-substrate:	0.115
CYP3A4-inhibitor:	0.898
CYP3A4-substrate:	0.199

ADMET: Excretion

Clearance (CL):	4.011
Half-life (T1/2):	0.301

ADMET: Toxicity

hERG Blockers:	0.025
Human Hepatotoxicity (H-HT):	0.138
Drug-inuced Liver Injury (DILI):	0.091
AMES Toxicity:	0.14
Rat Oral Acute Toxicity:	0.091
Maximum Recommended Daily Dose:	0.028
Skin Sensitization:	0.941
Carcinogencity:	0.394
Eye Corrosion:	0.926
Eye Irritation:	0.823
Respiratory Toxicity:	0.739

Download Data

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

Natural Product: NPC2354

Natural Product ID:	NPC2354
*Common Name:**	VRUFZWKTAKCFGU-FYPAKXHLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VRUFZWKTAKCFGU-FYPAKXHLSA-N
Standard InCHI:	InChI=1S/C18H30O4/c1-4-5-6-7-8-9-10-11-12-13-14-16(18(21)22-3)17(20)15(2)19/h4,14,17,20H,1,5-13H2,2-3H3/b16-14+/t17-/m1/s1
SMILES:	C=CCCCCCCCCC/C=C([C@@H](C(=O)C)O)/C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002951] Long-chain fatty alcohols

*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
NPO2324	Phoma herbarum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12713403]
NPO16241	Eucalyptus perriniana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23980409]
NPO16722	Tolypothrix nodosa	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8792625]
NPO16722	Tolypothrix nodosa	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9748382]
NPO10282	Solenostoma triste	Species	Solenostomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16722	Tolypothrix nodosa	Species	Tolypothrichaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2324	Phoma herbarum	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16587	Actinodaphne longifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15419	Tunica prolifera	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO17084	Marsilea quadrifolia	Species	Marsileaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15935	Pinus parviflora	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16241	Eucalyptus perriniana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13829	Cryptocarya angulata	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10869	Cota saguramica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17389	Papilio xuthus	Species	Papilionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17015	Plantago hookeriana	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17537	Anthotroche blackii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14831	Mastophora hutchinsoni	Species	Corallinaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC2354 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	181
0.1-0.2	1760
0.2-0.3	7457
0.3-0.4	16700
0.4-0.5	9996
0.5-0.6	4675
0.6-0.7	1647
0.7-0.8	275
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	3

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 NPC2354 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	157
0.1-0.2	2401
0.2-0.3	4010
0.3-0.4	1851
0.4-0.5	544
0.5-0.6	147
0.6-0.7	37
0.7-0.8	3
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