NPASS Compound

Structure

NPC138948 OpenBabel06302215242D 24 26 0 0 1 0 0 0 0 0999 V2000 4.1698 -3.3704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3358 -3.8519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5019 -3.3704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6679 -3.8519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5019 -2.4074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3358 -1.9259 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8340 -1.4444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8340 -0.4815 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6679 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5837 -0.2976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8813 -1.2134 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1497 0.4815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1127 0.4815 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5837 1.2605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6679 0.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8340 1.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8340 1.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6679 0.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6679 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8340 -0.4815 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8340 -1.4444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.9630 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 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 23 1 0 0 0 0 9 15 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 23 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 21 23 1 0 0 0 0 23 24 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	328.17
Volume:	348.149
LogP:	4.045
LogD:	4.071
LogS:	-4.513
# Rotatable Bonds:	3
TPSA:	59.67
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.669
Synthetic Accessibility Score:	4.751
Fsp3:	0.45
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.792
MDCK Permeability:	1.7562138964422047e-05
Pgp-inhibitor:	0.954
Pgp-substrate:	0.01
Human Intestinal Absorption (HIA):	0.012
20% Bioavailability (F20%):	0.679
30% Bioavailability (F30%):	0.516

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.127
Plasma Protein Binding (PPB):	96.52796173095703%
Volume Distribution (VD):	1.785
Pgp-substrate:	6.099417209625244%

ADMET: Metabolism

CYP1A2-inhibitor:	0.975
CYP1A2-substrate:	0.654
CYP2C19-inhibitor:	0.785
CYP2C19-substrate:	0.765
CYP2C9-inhibitor:	0.87
CYP2C9-substrate:	0.519
CYP2D6-inhibitor:	0.736
CYP2D6-substrate:	0.181
CYP3A4-inhibitor:	0.751
CYP3A4-substrate:	0.464

ADMET: Excretion

Clearance (CL):	8.074
Half-life (T1/2):	0.778

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.711
Drug-inuced Liver Injury (DILI):	0.179
AMES Toxicity:	0.027
Rat Oral Acute Toxicity:	0.612
Maximum Recommended Daily Dose:	0.641
Skin Sensitization:	0.962
Carcinogencity:	0.829
Eye Corrosion:	0.969
Eye Irritation:	0.449
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC138948

Natural Product ID:	NPC138948
*Common Name:**	IUILTPPQAYRTKI-VCVVZTQCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IUILTPPQAYRTKI-VCVVZTQCSA-N
Standard InCHI:	InChI=1S/C20H24O4/c1-6-11(2)18(21)24-17-16-13(4)19(22)23-15(16)10-14-9-7-8-12(3)20(14,17)5/h6,9-10,12,17H,7-8H2,1-5H3/b11-6-/t12-,17+,20+/m0/s1
SMILES:	C/C=C(/C)C(=O)O[C@@H]1C2=C(C)C(=O)OC2=CC2=CCC[C@H](C)[C@@]12C
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:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones

*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
NPO29103	Spongia matamata	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075761]
NPO28939	Piptanthus nepalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28939	Piptanthus nepalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28939	Piptanthus nepalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28974	Smilax ornata	Species	Staphylinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29103	Spongia matamata	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26540	Echinopsis spachiana	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29402	Launaea arborescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29194	Harziella entomophila	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO29013	Annulohypoxylon cohaerens	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25969	Aspergillus nomius	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28870	Clausena lenis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11524	Macrotomia ugamensis	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28808	Piptanthus mongolicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28939	Piptanthus nepalensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29157	Reichardia gaditana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28829	Pelvetia wrightii	Species	Fucaceae	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 NPC138948 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	202
0.1-0.2	1180
0.2-0.3	4608
0.3-0.4	12847
0.4-0.5	13206
0.5-0.6	7331
0.6-0.7	2906
0.7-0.8	391
0.8-0.85	17
0.85-0.9	9
0.9-0.95	0
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 NPC138948 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	179
0.1-0.2	1476
0.2-0.3	3839
0.3-0.4	2497
0.4-0.5	832
0.5-0.6	274
0.6-0.7	50
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