NPASS Compound

Structure

NPC4410 OpenBabel06302216012D 29 33 0 0 1 0 0 0 0 0999 V2000 -4.2208 -1.2367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2208 -0.2367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3198 0.1972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0973 1.1721 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.7208 1.9540 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4118 2.9050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4607 3.2140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2208 3.4928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2208 4.4928 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0298 2.9050 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7208 1.9540 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3443 1.1721 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1218 0.1972 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.9802 -0.3157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7333 0.3422 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3403 1.2618 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2137 1.7488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3552 2.2617 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7082 0.1197 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3884 0.8528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0936 1.8083 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.3633 0.6302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1224 1.3946 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4422 0.6616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7370 -0.2940 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4673 0.8841 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8621 1.8029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5320 0.8467 0.0000 C 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 1 2 2 0 0 0 0 2 13 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 4 23 1 1 0 0 0 5 6 1 6 0 0 0 5 11 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 11 10 1 1 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 16 1 0 0 0 0 13 14 1 6 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 19 1 6 0 0 0 16 18 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 29 1 0 0 0 0 26 27 1 0 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	458.38
Volume:	514.308
LogP:	6.108
LogD:	5.108
LogS:	-5.302
# Rotatable Bonds:	4
TPSA:	60.69
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.435
Synthetic Accessibility Score:	5.202
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.712
MDCK Permeability:	2.662222323124297e-05
Pgp-inhibitor:	0.958
Pgp-substrate:	0.632
Human Intestinal Absorption (HIA):	0.04
20% Bioavailability (F20%):	0.988
30% Bioavailability (F30%):	0.759

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.13
Plasma Protein Binding (PPB):	98.62195587158203%
Volume Distribution (VD):	1.182
Pgp-substrate:	3.1629011631011963%

ADMET: Metabolism

CYP1A2-inhibitor:	0.119
CYP1A2-substrate:	0.203
CYP2C19-inhibitor:	0.081
CYP2C19-substrate:	0.779
CYP2C9-inhibitor:	0.311
CYP2C9-substrate:	0.593
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.216
CYP3A4-inhibitor:	0.807
CYP3A4-substrate:	0.338

ADMET: Excretion

Clearance (CL):	7.78
Half-life (T1/2):	0.208

ADMET: Toxicity

hERG Blockers:	0.729
Human Hepatotoxicity (H-HT):	0.702
Drug-inuced Liver Injury (DILI):	0.04
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.426
Maximum Recommended Daily Dose:	0.138
Skin Sensitization:	0.933
Carcinogencity:	0.028
Eye Corrosion:	0.276
Eye Irritation:	0.415
Respiratory Toxicity:	0.934

Download Data

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

Natural Product: NPC4410

Natural Product ID:	NPC4410
*Common Name:**	ASFJLXDTSOQTGS-LHPNVNLSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ASFJLXDTSOQTGS-LHPNVNLSSA-N
Standard InCHI:	InChI=1S/C21H24O8/c1-9-5-13(28-19(24)20(4)7-25-20)15-10(2)18(23)29-17(15)16-12(9)6-14(27-11(3)22)21(16)8-26-21/h12-17H,1-2,5-8H2,3-4H3/t12-,13-,14-,15+,16-,17-,20-,21+/m0/s1
SMILES:	C=C1C[C@@H]([C@H]2C(=C)C(=O)O[C@@H]2[C@@H]2[C@H]1C[C@@H]([C@@]12CO1)OC(=O)C)OC(=O)[C@]1(C)CO1
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 [CHEMONTID:0001543] Sesquiterpene lactones [CHEMONTID:0001770] Guaianolides 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
NPO385	Bipolaris oryzae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23668986]
NPO22317	Crinum amabile	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8229016]
NPO22317	Crinum amabile	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7524	Albifimbria verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22317	Crinum amabile	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23041	Aplysia oculifera	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23458	Gustavia superba	Species	Lecythidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12427	Leucosyke quadrinervia	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22317	Crinum amabile	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO385	Bipolaris oryzae	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7524	Albifimbria verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24004	Centratherum punctatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24131	Cladonia rangiformis	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23544	Estigmene acrea	Species	Erebidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24333	Streptomyces chrestomyceticus	Species	Streptomycetaceae	Bacteria	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 NPC4410 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	361
0.1-0.2	2838
0.2-0.3	8744
0.3-0.4	15899
0.4-0.5	8665
0.5-0.6	4743
0.6-0.7	1172
0.7-0.8	237
0.8-0.85	34
0.85-0.9	3
0.9-0.95	1
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 NPC4410 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	417
0.1-0.2	3344
0.2-0.3	3692
0.3-0.4	1200
0.4-0.5	343
0.5-0.6	144
0.6-0.7	8
0.7-0.8	2
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