NPASS Compound

Structure

NPC213444 OpenBabel06302216132D 35 42 0 0 0 0 0 0 0 0999 V2000 3.4335 0.0188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5518 -0.4904 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5519 -1.4723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4029 -1.9633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4031 -2.9458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5523 -3.4371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7014 -2.9461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7012 -1.9637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8508 -1.4730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8504 -0.4907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7011 0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8503 1.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8499 2.4559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0005 2.9466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8512 2.4552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8511 1.4734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0004 0.9823 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 0.0006 -1.9640 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.0008 -2.9459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7306 -3.6027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5266 -4.5631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4071 -4.8667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1368 -4.2099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9329 -3.2495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5102 -2.4553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9332 -1.6608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3327 -0.7640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3092 -0.6615 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7087 0.2353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6852 0.3378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2621 -0.4567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8626 -1.3535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8862 -1.4560 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4866 -2.3528 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 11 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 19 1 0 0 0 0 10 18 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 17 1 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 19 27 1 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 35 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	448.17
Volume:	478.084
LogP:	6.886
LogD:	5.221
LogS:	-8.263
# Rotatable Bonds:	1
TPSA:	35.64
# H-Bond Aceptor:	4
# H-Bond Donor:	0
# Rings:	8
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.261
Synthetic Accessibility Score:	2.597
Fsp3:	0.032
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:	-5.021
MDCK Permeability:	1.6629002857371233e-05
Pgp-inhibitor:	0.99
Pgp-substrate:	0.563
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.973
30% Bioavailability (F30%):	0.356

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.052
Plasma Protein Binding (PPB):	97.9818115234375%
Volume Distribution (VD):	1.049
Pgp-substrate:	0.49746063351631165%

ADMET: Metabolism

CYP1A2-inhibitor:	0.891
CYP1A2-substrate:	0.215
CYP2C19-inhibitor:	0.624
CYP2C19-substrate:	0.087
CYP2C9-inhibitor:	0.418
CYP2C9-substrate:	0.833
CYP2D6-inhibitor:	0.022
CYP2D6-substrate:	0.832
CYP3A4-inhibitor:	0.354
CYP3A4-substrate:	0.525

ADMET: Excretion

Clearance (CL):	4.072
Half-life (T1/2):	0.108

ADMET: Toxicity

hERG Blockers:	0.096
Human Hepatotoxicity (H-HT):	0.658
Drug-inuced Liver Injury (DILI):	0.81
AMES Toxicity:	0.653
Rat Oral Acute Toxicity:	0.629
Maximum Recommended Daily Dose:	0.984
Skin Sensitization:	0.505
Carcinogencity:	0.903
Eye Corrosion:	0.003
Eye Irritation:	0.887
Respiratory Toxicity:	0.071

Download Data

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

Natural Product: NPC213444

Natural Product ID:	NPC213444
*Common Name:**	AAUYVWYMLDVLOW-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AAUYVWYMLDVLOW-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C31H20N4/c1-34-25-16-8-5-13-22(25)31(29-30(34)20-11-3-7-15-24(20)33-29)35-26-17-9-4-12-21(26)28-27(35)18-19-10-2-6-14-23(19)32-28/h2-18H,1H3
SMILES:	Cn1c2ccccc2c(c2-c1c1ccccc1n2)n1c2ccccc2c2c1cc1ccccc1n2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	9981100
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001253] Quinolines and derivatives [CHEMONTID:0000061] Indoloquinolines

*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
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[14640526]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	depth of 25 m off the shore of Keomun Island, Korea	2004-AUG	PMID[18407691]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2853205]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO20169	Alseodaphne perakensis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20989	Calea integrifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17131	Yucca periculosa	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20299	Strongylophora durissima	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO18755	Fumaria judaica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21890	Epidendrum moseni	Species	Orchidaceae	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 NPC213444 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	1331
0.1-0.2	13825
0.2-0.3	17932
0.3-0.4	4762
0.4-0.5	2068
0.5-0.6	1865
0.6-0.7	748
0.7-0.8	139
0.8-0.85	9
0.85-0.9	11
0.9-0.95	7
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 NPC213444 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	608
0.1-0.2	857
0.2-0.3	1085
0.3-0.4	2310
0.4-0.5	2050
0.5-0.6	1657
0.6-0.7	529
0.7-0.8	47
0.8-0.85	7
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