NPASS Compound

Structure

NPC299674 OpenBabel06302215502D 25 27 0 0 1 0 0 0 0 0999 V2000 -3.1758 -3.6286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1829 -3.5092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5831 -4.3093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9761 -5.2288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3763 -6.0290 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5903 -4.1899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0096 -4.9901 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1972 -3.2704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7971 -2.4703 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7782 -2.6635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5410 -2.0169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5111 -1.0174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3288 -0.4417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0341 0.5138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0342 0.5288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4586 1.3465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7110 -0.4175 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7431 -0.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3364 -1.5827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6581 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3272 -2.2213 0.0000 C 0 0 0 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 1.7796 -0.0933 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 -3.4546 -2.4237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 6 1 0 0 0 0 4 5 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 19 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 25 1 0 0 0 0 12 17 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 17 15 1 6 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 24 1 1 0 0 0 19 20 1 6 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	344.16
Volume:	356.939
LogP:	2.185
LogD:	1.421
LogS:	-2.896
# Rotatable Bonds:	4
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.484
Synthetic Accessibility Score:	4.784
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.604
MDCK Permeability:	2.391383532085456e-05
Pgp-inhibitor:	0.035
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.104
20% Bioavailability (F20%):	0.036
30% Bioavailability (F30%):	0.34

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.035
Plasma Protein Binding (PPB):	82.50958251953125%
Volume Distribution (VD):	2.665
Pgp-substrate:	9.10380744934082%

ADMET: Metabolism

CYP1A2-inhibitor:	0.249
CYP1A2-substrate:	0.088
CYP2C19-inhibitor:	0.39
CYP2C19-substrate:	0.221
CYP2C9-inhibitor:	0.623
CYP2C9-substrate:	0.081
CYP2D6-inhibitor:	0.022
CYP2D6-substrate:	0.066
CYP3A4-inhibitor:	0.735
CYP3A4-substrate:	0.171

ADMET: Excretion

Clearance (CL):	11.571
Half-life (T1/2):	0.662

ADMET: Toxicity

hERG Blockers:	0.012
Human Hepatotoxicity (H-HT):	0.708
Drug-inuced Liver Injury (DILI):	0.838
AMES Toxicity:	0.148
Rat Oral Acute Toxicity:	0.76
Maximum Recommended Daily Dose:	0.746
Skin Sensitization:	0.886
Carcinogencity:	0.257
Eye Corrosion:	0.142
Eye Irritation:	0.124
Respiratory Toxicity:	0.952

Download Data

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

Natural Product: NPC299674

Natural Product ID:	NPC299674
*Common Name:**	FVFUKWZLGLEYBQ-XYFCJCGZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FVFUKWZLGLEYBQ-XYFCJCGZSA-N
Standard InCHI:	InChI=1S/C20H24O5/c1-5-13(9-21)20(23)24-15-8-11(3)14-7-6-10(2)16(14)18-17(15)12(4)19(22)25-18/h5-6,15-18,21H,4,7-9H2,1-3H3/b13-5-/t15-,16+,17-,18-/m1/s1
SMILES:	C/C=C(/CO)C(=O)O[C@@H]1CC(=C2CC=C(C)[C@@H]2[C@@H]2[C@@H]1C(=C)C(=O)O2)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101318101
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000472] Hydroxy acids and derivatives [CHEMONTID:0001713] Beta hydroxy acids and derivatives

*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
NPO23542	Omphalotus illudens	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11087609]
NPO23542	Omphalotus illudens	Species	Omphalotaceae	Eukaryota	mature fruiting bodies	n.a.	n.a.	PMID[14510611]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3885	Ampulloclitocybe clavipes	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23918	Cochlearia armoracia	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23542	Omphalotus illudens	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23832	Cyclea sutchuenensis	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3885	Ampulloclitocybe clavipes	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24088	Senecio glutinosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23316	Lappula anocarpa	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17405	Cinnamomum iners	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21959	Syncarpia glomulifera	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22805	Saussurea japonica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23959	Echium humile	Species	Boraginaceae	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 NPC299674 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	1128
0.2-0.3	4710
0.3-0.4	10121
0.4-0.5	14034
0.5-0.6	7040
0.6-0.7	4026
0.7-0.8	1194
0.8-0.85	160
0.85-0.9	79
0.9-0.95	13
0.95-1	0

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 NPC299674 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	175
0.1-0.2	1677
0.2-0.3	3662
0.3-0.4	2448
0.4-0.5	745
0.5-0.6	347
0.6-0.7	70
0.7-0.8	23
0.8-0.85	3
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