NPASS Compound

Structure

NPC307408 OpenBabel06302215192D 36 39 0 0 1 0 0 0 0 0999 V2000 6.2701 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4041 -0.9781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.5380 -1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5380 -2.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6720 -2.9781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8060 -2.4781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8060 -1.4781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6720 -0.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6720 0.0219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9400 -0.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0739 -1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2079 -0.9781 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6581 -1.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6581 -2.4781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2079 -2.9781 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2079 -3.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6581 -4.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0739 -2.4781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5241 -2.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4013 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9945 0.1045 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4945 0.9706 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9945 1.8366 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9945 1.8366 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4945 2.7026 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5055 2.7026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9945 3.5686 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4945 4.4347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4945 0.9706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4945 2.7026 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4945 0.9706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4945 -0.7615 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 1.9400 -2.9781 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6720 -3.9781 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 1 0 0 0 3 4 1 0 0 0 0 3 8 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 36 1 6 0 0 0 6 7 1 0 0 0 0 6 35 1 1 0 0 0 7 8 1 0 0 0 0 7 10 1 1 0 0 0 8 9 1 6 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 13 1 0 0 0 0 12 34 1 6 0 0 0 13 14 1 0 0 0 0 13 20 1 1 0 0 0 14 15 1 0 0 0 0 14 19 1 1 0 0 0 15 16 1 6 0 0 0 15 18 1 0 0 0 0 16 17 1 0 0 0 0 21 20 1 1 0 0 0 21 30 1 0 0 0 0 21 22 1 0 0 0 0 21 34 1 0 0 0 0 22 23 1 0 0 0 0 22 33 1 6 0 0 0 23 24 1 0 0 0 0 23 32 1 6 0 0 0 24 25 1 0 0 0 0 24 31 1 1 0 0 0 25 26 1 1 0 0 0 25 30 1 0 0 0 0 26 27 1 6 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	527.23
Volume:	467.514
LogP:	-2.056
LogD:	-1.739
LogS:	-2.038
# Rotatable Bonds:	6
TPSA:	250.06
# H-Bond Aceptor:	16
# H-Bond Donor:	11
# Rings:	4
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.146
Synthetic Accessibility Score:	6.195
Fsp3:	1.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.258
MDCK Permeability:	0.00020609247440006584
Pgp-inhibitor:	0.002
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	1.0
20% Bioavailability (F20%):	0.999
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.244
Plasma Protein Binding (PPB):	17.463668823242188%
Volume Distribution (VD):	0.314
Pgp-substrate:	82.03553009033203%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.074
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.003
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.12
CYP3A4-inhibitor:	0.004
CYP3A4-substrate:	0.014

ADMET: Excretion

Clearance (CL):	0.929
Half-life (T1/2):	0.785

ADMET: Toxicity

hERG Blockers:	0.245
Human Hepatotoxicity (H-HT):	0.424
Drug-inuced Liver Injury (DILI):	0.025
AMES Toxicity:	0.168
Rat Oral Acute Toxicity:	0.069
Maximum Recommended Daily Dose:	0.015
Skin Sensitization:	0.846
Carcinogencity:	0.033
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.962

Download Data

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

Natural Product: NPC307408

Natural Product ID:	NPC307408
*Common Name:**	SVCCPSYPFRZFPC-KERCXNEUSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SVCCPSYPFRZFPC-KERCXNEUSA-N
Standard InCHI:	InChI=1S/C20H37N3O13/c1-23-6-4-5(21)7(24)12(8(6)25)32-19-15-13(11(28)18(31-3)33-19)34-20(36-15)16(29)10(27)9(26)14(35-20)17(22)30-2/h5-19,23-29H,4,21-22H2,1-3H3/t5-,6-,7+,8+,9+,10+,11-,12+,13+,14-,15-,16+,17-,18-,19+,20-/m0/s1
SMILES:	CN[C@H]1C[C@@H]([C@H]([C@H]([C@@H]1O)O[C@H]1[C@@H]2[C@@H]([C@@H]([C@@H](OC)O1)O)O[C@]1([C@@H]([C@@H]([C@H]([C@@H]([C@@H](N)OC)O1)O)O)O)O2)O)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO6984	Brickellia veronicaefolia	Species	Asteraceae	Eukaryota	essential oil	n.a.	n.a.	PMID[16933870]
NPO695	Picea sitchensis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO695	Picea sitchensis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12143	Corydalis solida	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO695	Picea sitchensis	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1845	Physocarpus opulifolius	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3712	Pedicularis olgae	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12143	Corydalis solida	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8183	Asplenium viviparum	Species	Aspleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO254	Coreopsis capillacea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5089	Abies forrestii	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6814	Pegaeophyton scapiflorum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2531	Daniellia oliveri	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6984	Brickellia veronicaefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6636	Ophiorrhiza filistipula	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4093	Astragalus stipulosus	Species	Fabaceae	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 NPC307408 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	324
0.1-0.2	10921
0.2-0.3	19386
0.3-0.4	9310
0.4-0.5	2400
0.5-0.6	255
0.6-0.7	57
0.7-0.8	19
0.8-0.85	7
0.85-0.9	15
0.9-0.95	2
0.95-1	1

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 NPC307408 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	95
0.1-0.2	3039
0.2-0.3	4531
0.3-0.4	1139
0.4-0.5	205
0.5-0.6	77
0.6-0.7	27
0.7-0.8	15
0.8-0.85	8
0.85-0.9	11
0.9-0.95	3
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