NPASS Compound

Structure

CID193906 OpenBabel06191715582D 30 34 0 0 1 0 0 0 0 0999 V2000 -0.8660 -1.5000 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 5.1962 0.0000 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 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 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 3.4641 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 -1.7321 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 -4.1369 2.0000 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 2.5000 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 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 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 2.5000 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 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 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 0.0000 -0.0000 0.0000 N 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 4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 2.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5491 1.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 25 1 0 0 0 0 3 27 1 0 0 0 0 4 28 1 0 0 0 0 5 6 2 0 0 0 0 5 14 1 0 0 0 0 6 16 1 0 0 0 0 7 8 2 0 0 0 0 7 15 1 0 0 0 0 8 19 1 0 0 0 0 9 13 1 0 0 0 0 10 14 2 0 0 0 0 10 20 1 0 0 0 0 11 17 2 0 0 0 0 11 21 1 0 0 0 0 12 29 1 0 0 0 0 12 30 1 0 0 0 0 13 26 2 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 15 22 2 0 0 0 0 16 23 2 0 0 0 0 17 23 1 0 0 0 0 18 9 1 6 0 0 0 18 22 1 0 0 0 0 18 25 1 0 0 0 0 19 24 2 0 0 0 0 19 27 1 0 0 0 0 20 21 2 0 0 0 0 20 29 1 0 0 0 0 21 30 1 0 0 0 0 22 24 1 0 0 0 0 23 25 1 0 0 0 0 24 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	405.16
Volume:	412.098
LogP:	4.442
LogD:	3.544
LogS:	-6.571
# Rotatable Bonds:	4
TPSA:	57.23
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.626
Synthetic Accessibility Score:	3.263
Fsp3:	0.292
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.841
MDCK Permeability:	6.653877790085971e-05
Pgp-inhibitor:	0.197
Pgp-substrate:	0.595
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.897

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.143
Plasma Protein Binding (PPB):	91.98332977294922%
Volume Distribution (VD):	0.741
Pgp-substrate:	2.6408870220184326%

ADMET: Metabolism

CYP1A2-inhibitor:	0.889
CYP1A2-substrate:	0.931
CYP2C19-inhibitor:	0.975
CYP2C19-substrate:	0.845
CYP2C9-inhibitor:	0.867
CYP2C9-substrate:	0.916
CYP2D6-inhibitor:	0.938
CYP2D6-substrate:	0.931
CYP3A4-inhibitor:	0.904
CYP3A4-substrate:	0.889

ADMET: Excretion

Clearance (CL):	12.585
Half-life (T1/2):	0.151

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.213
Drug-inuced Liver Injury (DILI):	0.894
AMES Toxicity:	0.679
Rat Oral Acute Toxicity:	0.263
Maximum Recommended Daily Dose:	0.972
Skin Sensitization:	0.29
Carcinogencity:	0.921
Eye Corrosion:	0.003
Eye Irritation:	0.054
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC193906

Natural Product ID:	NPC193906
*Common Name:**	6-Acetonyldihydrochelerythrine
IUPAC Name:	1-[(13S)-1,2-dimethoxy-12-methyl-13H-[1,3]benzodioxolo[5,6-c]phenanthridin-13-yl]propan-2-one
Synonyms:	6-Acetonyldihydrochelerythrine
Standard InCHIKey:	VGTQLFWIJIABSU-SFHVURJKSA-N
Standard InCHI:	InChI=1S/C24H23NO5/c1-13(26)9-18-22-15(7-8-19(27-3)24(22)28-4)16-6-5-14-10-20-21(30-12-29-20)11-17(14)23(16)25(18)2/h5-8,10-11,18H,9,12H2,1-4H3/t18-/m0/s1
SMILES:	COc1c(OC)ccc2c1[C@H](CC(=O)C)N(C)c1c2ccc2c1cc1OCOc1c2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL250267
PubChem CID:	185516
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002665] Benzophenanthridine alkaloids [CHEMONTID:0002667] Dihydrobenzophenanthridine 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3504	Argemone mexicana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21094631]
NPO2842	Garcinia lucida	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17880175]
NPO5515	Cephalocroton cordofanus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20801	Antrodia sinuosa	Species	Fomitopsidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2842	Garcinia lucida	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9944	Salisaeta longa	Species	Rhodothermaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3504	Argemone mexicana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5348	Colletotrichum acutatum	Species	Glomerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6338	Chilo auricilius	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3504	Argemone mexicana	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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	5
Others	15

Activity Type	# Activity
Cell Line	9
NON-MOLECULAR	5
Organism	6

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT323	Cell Line	SW-620	Homo sapiens	Activity	=	27.0	%	PMID[575438]
NPT393	Cell Line	HCT-116	Homo sapiens	Activity	=	22.0	%	PMID[575438]
NPT323	Cell Line	SW-620	Homo sapiens	Activity	=	22.0	%	PMID[575438]
NPT393	Cell Line	HCT-116	Homo sapiens	Activity	=	19.0	%	PMID[575438]
NPT323	Cell Line	SW-620	Homo sapiens	Activity	=	65.0	%	PMID[575438]
NPT323	Cell Line	SW-620	Homo sapiens	Activity	=	34.0	%	PMID[575438]
NPT323	Cell Line	SW-620	Homo sapiens	FC	=	1.1	n.a.	PMID[575438]
NPT323	Cell Line	SW-620	Homo sapiens	IC50	=	3800.0	nM	PMID[575438]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	65.0	%	PMID[575438]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	=	25.0	%	PMID[575438]

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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 NPC193906 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	378
0.1-0.2	1829
0.2-0.3	7790
0.3-0.4	9608
0.4-0.5	6758
0.5-0.6	13896
0.6-0.7	1824
0.7-0.8	568
0.8-0.85	28
0.85-0.9	11
0.9-0.95	5
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC23080
0.9314	High Similarity	NPC179704
0.9231	High Similarity	NPC17677
0.9143	High Similarity	NPC287588
0.8978	High Similarity	NPC471489

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 NPC193906 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	240
0.1-0.2	726
0.2-0.3	893
0.3-0.4	1600
0.4-0.5	2846
0.5-0.6	2218
0.6-0.7	567
0.7-0.8	60
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.841	Intermediate Similarity	NPD4859	Phase 1
0.7826	Intermediate Similarity	NPD3763	Approved
0.7697	Intermediate Similarity	NPD3641	Approved
0.7697	Intermediate Similarity	NPD3639	Approved
0.7697	Intermediate Similarity	NPD3640	Phase 3

Showing 1 to 5 of 200 entries

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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