NPASS Compound

Structure

NPC39573 OpenBabel06302215072D 29 34 0 0 1 0 0 0 0 0999 V2000 -1.9578 1.4318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0747 1.4175 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6207 2.1751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2624 2.1608 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 0.8640 2.8075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6650 2.4352 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2707 2.2908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6418 1.7909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6048 1.1693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1769 0.7170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5505 1.0851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6183 1.5509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0248 1.7883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4638 1.6185 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9184 0.7266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9129 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5584 0.6455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5584 1.5584 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2636 2.0198 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6916 1.3888 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2376 0.6312 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6455 0.6455 0.0000 C 0 0 1 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 -0.3380 -0.8160 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5242 0.5559 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1276 2.5164 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8959 2.0806 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1209 3.3996 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8824 3.8470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 22 1 0 0 0 0 3 4 1 0 0 0 0 4 20 1 0 0 0 0 4 5 1 0 0 0 0 6 5 1 1 0 0 0 6 7 1 0 0 0 0 6 18 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 14 1 0 0 0 0 9 10 2 0 0 0 0 10 17 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 15 2 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 15 26 1 0 0 0 0 16 23 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 20 1 0 0 0 0 20 21 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 22 25 1 6 0 0 0 23 24 2 0 0 0 0 26 27 2 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:	395.17
Volume:	394.155
LogP:	2.163
LogD:	2.151
LogS:	-3.978
# Rotatable Bonds:	2
TPSA:	79.98
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.748
Synthetic Accessibility Score:	5.564
Fsp3:	0.565
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.365
MDCK Permeability:	2.3310409233090468e-05
Pgp-inhibitor:	0.029
Pgp-substrate:	0.987
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.188
30% Bioavailability (F30%):	0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.344
Plasma Protein Binding (PPB):	81.80258178710938%
Volume Distribution (VD):	1.889
Pgp-substrate:	13.441408157348633%

ADMET: Metabolism

CYP1A2-inhibitor:	0.286
CYP1A2-substrate:	0.751
CYP2C19-inhibitor:	0.102
CYP2C19-substrate:	0.809
CYP2C9-inhibitor:	0.21
CYP2C9-substrate:	0.113
CYP2D6-inhibitor:	0.494
CYP2D6-substrate:	0.657
CYP3A4-inhibitor:	0.424
CYP3A4-substrate:	0.767

ADMET: Excretion

Clearance (CL):	13.288
Half-life (T1/2):	0.026

ADMET: Toxicity

hERG Blockers:	0.87
Human Hepatotoxicity (H-HT):	0.663
Drug-inuced Liver Injury (DILI):	0.31
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.571
Maximum Recommended Daily Dose:	0.922
Skin Sensitization:	0.326
Carcinogencity:	0.897
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.967

Download Data

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

Natural Product: NPC39573

Natural Product ID:	NPC39573
*Common Name:**	JHCADBPJWZOJRG-VBIFSVJFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JHCADBPJWZOJRG-VBIFSVJFSA-N
Standard InCHI:	InChI=1S/C23H25NO5/c1-11-9-24-10-12-4-5-14-16-13(6-7-29-14)17(21(26)28-3)18-19(16)22(12,2)15(24)8-23(11,27)20(18)25/h6-7,11-12,15,27H,4-5,8-10H2,1-3H3/t11-,12-,15-,22-,23+/m1/s1
SMILES:	C[C@@H]1CN2C[C@H]3CCc4c5-c(cco4)c(c4c5[C@@]3(C)[C@H]2C[C@]1(C4=O)O)C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	24764127
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0002937] Cycloheptapyrans

*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
NPO2863	Macaranga mappa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170679]
NPO1284	Neocheiropteris palmatopedata	Species	Polypodiaceae	Eukaryota	n.a.	root	n.a.	PMID[20100622]
NPO4333	Neorautanenia edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19849.1	Melilotus officinalis subsp. suaveolens	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8017	Tonduzia pittieri	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9584	Delphinium zalil	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9341	Chaetomium abuense	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10259	Aralia cordata	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7405	Candelaria medians	Species	Candelariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4333	Neorautanenia edulis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2005	Rungia repens	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2863	Macaranga mappa	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3332	Rhaponticum integrifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19849.1	Melilotus officinalis subsp. suaveolens	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1284	Neocheiropteris palmatopedata	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14943	Aphanamixis rohituka	Species	Meliaceae	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 NPC39573 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	250
0.1-0.2	1097
0.2-0.3	3521
0.3-0.4	9726
0.4-0.5	10956
0.5-0.6	13509
0.6-0.7	3592
0.7-0.8	46
0.8-0.85	0
0.85-0.9	0
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 NPC39573 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	176
0.1-0.2	557
0.2-0.3	1258
0.3-0.4	2267
0.4-0.5	2741
0.5-0.6	1743
0.6-0.7	403
0.7-0.8	5
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