NPASS Compound

Structure

NPC255552 OpenBabel06302216012D 26 30 0 0 1 0 0 0 0 0999 V2000 1.2238 1.0566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6435 0.5927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 0.9643 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5449 1.4695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4896 2.2103 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1241 2.6290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8341 2.4102 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -1.6691 2.8923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5037 2.4105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5039 1.4467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3391 0.9650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1741 1.4471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0087 0.9653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0089 0.0010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1745 -0.4811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3393 0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6696 0.0003 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6695 0.9646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8343 1.4464 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8347 -0.4817 0.0000 C 0 0 2 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 -0.8349 -1.4455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5114 -2.1318 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0977 -1.6882 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3539 -2.6172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0184 -0.9530 0.0000 O 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 21 1 0 0 0 0 3 4 1 0 0 0 0 3 19 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 19 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 18 2 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 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 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 20 1 0 0 0 0 19 18 1 1 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 26 1 1 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	231.11
Volume:	223.735
LogP:	0.068
LogD:	-0.289
LogS:	-2.86
# Rotatable Bonds:	2
TPSA:	99.69
# H-Bond Aceptor:	6
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.426
Synthetic Accessibility Score:	3.254
Fsp3:	0.273
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:	-5.459
MDCK Permeability:	2.7715079795598285e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.264
20% Bioavailability (F20%):	0.039
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.616
Plasma Protein Binding (PPB):	35.97618865966797%
Volume Distribution (VD):	1.76
Pgp-substrate:	53.34290313720703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.126
CYP1A2-substrate:	0.657
CYP2C19-inhibitor:	0.066
CYP2C19-substrate:	0.073
CYP2C9-inhibitor:	0.018
CYP2C9-substrate:	0.416
CYP2D6-inhibitor:	0.433
CYP2D6-substrate:	0.754
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.087

ADMET: Excretion

Clearance (CL):	6.077
Half-life (T1/2):	0.688

ADMET: Toxicity

hERG Blockers:	0.313
Human Hepatotoxicity (H-HT):	0.358
Drug-inuced Liver Injury (DILI):	0.523
AMES Toxicity:	0.943
Rat Oral Acute Toxicity:	0.821
Maximum Recommended Daily Dose:	0.889
Skin Sensitization:	0.331
Carcinogencity:	0.846
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.941

Download Data

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

Natural Product: NPC255552

Natural Product ID:	NPC255552
*Common Name:**	RXPRRQLKFXBCSJ-NRSPTQNISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	RXPRRQLKFXBCSJ-NRSPTQNISA-N
Standard InCHI:	InChI=1S/C21H26N2O3/c1-3-20-10-6-11-22-12-9-15-14-7-4-5-8-16(14)23(17(15)18(20)22)21(25,13-20)19(24)26-2/h4-5,7-8,18,25H,3,6,9-13H2,1-2H3/t18-,20-,21+/m1/s1
SMILES:	CC[C@@]12CCCN3CCc4c5ccccc5n(c4[C@H]23)[C@](C1)(C(=O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	969508
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002671] Eburnan-type alkaloids

*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
NPO14590	Ruta oreojasme	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12216	Gynura elliptica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14590	Ruta oreojasme	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25628.1	Abrus pulchellus subsp. cantoniensis	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO14210	Brugmansia arborea	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13601	Relicina connivens	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25628.1	Abrus pulchellus subsp. cantoniensis	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19809	Streptomyces roseoviolaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3078	Gentiana pyrenaica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11862	Ostrinia nubilalis	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12216	Gynura elliptica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6602	Vinca major	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25599	Gloxinia erinoides	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1409	Drymonia macrophylla	Species	Gesneriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2065	Eriostemon deserti	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21627	Bambusa chungii	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13490	Diospyros tricolor	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14590	Ruta oreojasme	Species	Rutaceae	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 NPC255552 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	246
0.1-0.2	1243
0.2-0.3	7553
0.3-0.4	23268
0.4-0.5	4983
0.5-0.6	2849
0.6-0.7	2157
0.7-0.8	339
0.8-0.85	45
0.85-0.9	8
0.9-0.95	1
0.95-1	5

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 NPC255552 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	166
0.1-0.2	423
0.2-0.3	666
0.3-0.4	1651
0.4-0.5	2541
0.5-0.6	2705
0.6-0.7	877
0.7-0.8	116
0.8-0.85	3
0.85-0.9	0
0.9-0.95	1
0.95-1	1

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