NPASS Compound

Structure

NPC317905 OpenBabel06302215222D 23 27 0 0 1 0 0 0 0 0999 V2000 -4.0063 1.3559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0928 1.7626 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2838 1.1748 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -2.3883 0.1803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5793 -0.4075 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -0.8292 0.0717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7361 0.9569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3702 1.5816 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.5612 0.9938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6657 -0.0007 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8133 -0.4620 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.0136 -1.8699 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8266 -2.3317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6271 -1.8695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6263 -0.9238 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7997 -1.4079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6184 -1.8815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4378 -1.4093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4386 -0.4636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6200 0.0100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8005 -0.4622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4743 -2.7288 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 8 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 1 0 0 0 0 5 6 1 0 0 0 0 6 7 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 11 1 0 0 0 0 11 15 1 0 0 0 0 11 22 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 16 1 0 0 0 0 12 23 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 16 21 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	312.18
Volume:	323.426
LogP:	2.559
LogD:	2.541
LogS:	-3.934
# Rotatable Bonds:	2
TPSA:	44.73
# H-Bond Aceptor:	4
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.823
Synthetic Accessibility Score:	5.381
Fsp3:	0.579
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:	-4.627
MDCK Permeability:	3.02208136417903e-05
Pgp-inhibitor:	0.016
Pgp-substrate:	0.047
Human Intestinal Absorption (HIA):	0.224
20% Bioavailability (F20%):	0.077
30% Bioavailability (F30%):	0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.988
Plasma Protein Binding (PPB):	70.89108276367188%
Volume Distribution (VD):	2.72
Pgp-substrate:	26.50040626525879%

ADMET: Metabolism

CYP1A2-inhibitor:	0.051
CYP1A2-substrate:	0.632
CYP2C19-inhibitor:	0.142
CYP2C19-substrate:	0.877
CYP2C9-inhibitor:	0.18
CYP2C9-substrate:	0.174
CYP2D6-inhibitor:	0.345
CYP2D6-substrate:	0.877
CYP3A4-inhibitor:	0.778
CYP3A4-substrate:	0.91

ADMET: Excretion

Clearance (CL):	11.408
Half-life (T1/2):	0.088

ADMET: Toxicity

hERG Blockers:	0.056
Human Hepatotoxicity (H-HT):	0.434
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.096
Rat Oral Acute Toxicity:	0.455
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.062
Carcinogencity:	0.914
Eye Corrosion:	0.003
Eye Irritation:	0.009
Respiratory Toxicity:	0.723

Download Data

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

Natural Product: NPC317905

Natural Product ID:	NPC317905
*Common Name:**	ALNKTVLUDWIWIH-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ALNKTVLUDWIWIH-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C19H24N2O2/c1-2-13-12-21-9-7-14(13)11-17(21)19-18(22,8-10-23-19)15-5-3-4-6-16(15)20-19/h2-6,13-14,17,20,22H,1,7-12H2
SMILES:	C=CC1CN2CCC1CC2C34C(CCO3)(C5=CC=CC=C5N4)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	157080
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0001146] Indolines

*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
NPO30377	Cinchona ledgeriana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30377	Cinchona ledgeriana	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]

☑ 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 NPC317905 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

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 NPC317905 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

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