NPASS Compound

Structure

CID285254 OpenBabel06191716092D 31 33 0 0 0 0 0 0 0 0999 V2000 3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 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 1.7321 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 13 1 0 0 0 0 3 14 1 0 0 0 0 4 14 1 0 0 0 0 5 26 1 0 0 0 0 6 31 1 0 0 0 0 7 9 1 0 0 0 0 7 13 2 0 0 0 0 8 11 1 0 0 0 0 8 14 2 0 0 0 0 9 15 1 0 0 0 0 10 12 2 0 0 0 0 10 15 1 0 0 0 0 11 16 1 0 0 0 0 12 17 1 0 0 0 0 15 18 2 0 0 0 0 16 22 2 0 0 0 0 16 23 1 0 0 0 0 17 20 2 0 0 0 0 17 27 1 0 0 0 0 18 20 1 0 0 0 0 18 24 1 0 0 0 0 19 21 2 0 0 0 0 19 22 1 0 0 0 0 19 24 1 0 0 0 0 20 26 1 0 0 0 0 21 25 1 0 0 0 0 21 26 1 0 0 0 0 22 28 1 0 0 0 0 23 25 2 0 0 0 0 23 29 1 0 0 0 0 24 30 2 0 0 0 0 25 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	423.2
Volume:	446.506
LogP:	5.949
LogD:	3.128
LogS:	-3.112
# Rotatable Bonds:	5
TPSA:	91.92
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.404
Synthetic Accessibility Score:	3.331
Fsp3:	0.32
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	2
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.798
MDCK Permeability:	1.1891360372828785e-05
Pgp-inhibitor:	0.836
Pgp-substrate:	0.655
Human Intestinal Absorption (HIA):	0.36
20% Bioavailability (F20%):	0.701
30% Bioavailability (F30%):	0.084

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	83.96500396728516%
Volume Distribution (VD):	0.634
Pgp-substrate:	12.507452011108398%

ADMET: Metabolism

CYP1A2-inhibitor:	0.496
CYP1A2-substrate:	0.391
CYP2C19-inhibitor:	0.8
CYP2C19-substrate:	0.138
CYP2C9-inhibitor:	0.863
CYP2C9-substrate:	0.926
CYP2D6-inhibitor:	0.587
CYP2D6-substrate:	0.245
CYP3A4-inhibitor:	0.158
CYP3A4-substrate:	0.082

ADMET: Excretion

Clearance (CL):	3.927
Half-life (T1/2):	0.236

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.8
Drug-inuced Liver Injury (DILI):	0.174
AMES Toxicity:	0.62
Rat Oral Acute Toxicity:	0.31
Maximum Recommended Daily Dose:	0.236
Skin Sensitization:	0.777
Carcinogencity:	0.503
Eye Corrosion:	0.003
Eye Irritation:	0.867
Respiratory Toxicity:	0.384

Download Data

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

Natural Product: NPC285254

Natural Product ID:	NPC285254
*Common Name:**	1,3,5-Trihydroxy-4-Methoxy-10-Methyl-2,8-Bis(3-Methylbut-2-Enyl)Acridin-9-One
IUPAC Name:	1,3,5-trihydroxy-4-methoxy-10-methyl-2,8-bis(3-methylbut-2-enyl)acridin-9-one
Synonyms:
Standard InCHIKey:	LICNIJQEAUQKSD-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C25H29NO5/c1-13(2)7-9-15-10-12-17(27)20-18(15)24(30)19-21(26(20)5)25(31-6)23(29)16(22(19)28)11-8-14(3)4/h7-8,10,12,27-29H,9,11H2,1-6H3
SMILES:	COc1c(O)c(CC=C(C)C)c(c2c1n(C)c1c(c2=O)c(CC=C(C)C)ccc1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1668597
PubChem CID:	53316985
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001253] Quinolines and derivatives [CHEMONTID:0001908] Benzoquinolines [CHEMONTID:0000274] Acridines [CHEMONTID:0001811] Acridones

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO7221	Korolkowia sewerzowi	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2786	Clematis flammula	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5476	Hortia arborea	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10647	Gentiana lactea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5476	Hortia arborea	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO10647	Gentiana lactea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10647	Gentiana lactea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10647	Gentiana lactea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

Showing 1 to 8 of 8 entries

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
IC50	1
Ki	1

Activity Type	# Activity
Individual Protein	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT601	Individual Protein	Cathepsin L2	Homo sapiens	IC50	=	2500.0	nM	PMID[457130]
NPT601	Individual Protein	Cathepsin L2	Homo sapiens	Ki	=	500.0	nM	PMID[457130]

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☑ 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 NPC285254 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	558
0.1-0.2	2862
0.2-0.3	11835
0.3-0.4	5799
0.4-0.5	8519
0.5-0.6	10781
0.6-0.7	2063
0.7-0.8	232
0.8-0.85	21
0.85-0.9	17
0.9-0.95	8
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9701	High Similarity	NPC7560
0.9403	High Similarity	NPC2905
0.9353	High Similarity	NPC114468
0.9317	High Similarity	NPC76478
0.9307	High Similarity	NPC148391

Showing 1 to 5 of 200 entries

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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 NPC285254 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	332
0.1-0.2	687
0.2-0.3	1184
0.3-0.4	2007
0.4-0.5	2673
0.5-0.6	1784
0.6-0.7	446
0.7-0.8	36
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.922	High Similarity	NPD2899	Discontinued
0.7729	Intermediate Similarity	NPD6625	Approved
0.7652	Intermediate Similarity	NPD7922	Phase 1
0.7454	Intermediate Similarity	NPD7501	Clinical (unspecified phase)
0.7401	Intermediate Similarity	NPD7858	Clinical (unspecified phase)

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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