NPASS Compound

Structure

NPC488038 OpenBabel06302216142D 27 31 0 0 1 0 0 0 0 0999 V2000 2.7231 0.4010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3943 -0.6110 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.0388 -1.4982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3942 -2.3854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3512 -2.0465 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1849 -1.6059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3602 -0.6795 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7452 0.0352 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8029 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3512 -0.9498 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4015 -0.4015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5484 -0.9498 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5484 -2.0465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4982 -2.5948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4982 -3.6916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5484 -4.2399 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4014 -3.6916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4014 -2.5948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3229 -4.2236 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5484 -5.3040 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4699 -5.8360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4015 0.6953 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3621 0.9435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1707 1.0105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2281 1.1296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3880 -0.4041 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 10 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 6 0 0 0 5 18 1 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 27 1 1 0 0 0 8 9 1 0 0 0 0 8 25 1 1 0 0 0 9 22 1 0 0 0 0 9 10 1 0 0 0 0 9 23 1 1 0 0 0 10 11 1 6 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 22 1 0 0 0 0 13 18 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 2 0 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 20 21 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	377.18
Volume:	367.523
LogP:	1.516
LogD:	1.527
LogS:	-2.655
# Rotatable Bonds:	3
TPSA:	80.62
# H-Bond Aceptor:	7
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.822
Synthetic Accessibility Score:	6.104
Fsp3:	0.7
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.655
MDCK Permeability:	1.5696426999056712e-05
Pgp-inhibitor:	0.137
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.055
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.86

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.924
Plasma Protein Binding (PPB):	25.803592681884766%
Volume Distribution (VD):	1.977
Pgp-substrate:	60.599571228027344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.986
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.939
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.206
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.727
CYP3A4-inhibitor:	0.067
CYP3A4-substrate:	0.949

ADMET: Excretion

Clearance (CL):	15.297
Half-life (T1/2):	0.15

ADMET: Toxicity

hERG Blockers:	0.037
Human Hepatotoxicity (H-HT):	0.551
Drug-inuced Liver Injury (DILI):	0.055
AMES Toxicity:	0.709
Rat Oral Acute Toxicity:	0.63
Maximum Recommended Daily Dose:	0.845
Skin Sensitization:	0.741
Carcinogencity:	0.963
Eye Corrosion:	0.005
Eye Irritation:	0.017
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC488038

Natural Product ID:	NPC488038
*Common Name:**	GAUBYMMEBUOLGW-HMOIBATMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	GAUBYMMEBUOLGW-HMOIBATMSA-N
Standard InCHI:	InChI=1S/C20H27NO6/c1-21-8-7-18-9-12(22)17(25-3)20(26-4)19(18,21)10-14(27-20)11-5-6-13(24-2)16(23)15(11)18/h5-6,12,14,17,22-23H,7-10H2,1-4H3/t12-,14-,17-,18-,19-,20+/m0/s1
SMILES:	CN1CC[C@]23C[C@@H]([C@@H]([C@@]4([C@@]13C[C@@H](c1ccc(c(c21)O)OC)O4)OC)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	46888612
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002792] Hasubanan 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
NPO11351	Stephania japonica	Species	Menispermaceae	Eukaryota	Aerial parts	n.a.	n.a.	PMID[20426456]
NPO11351	Stephania japonica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9392886]
NPO11351	Stephania japonica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11351	Stephania japonica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11351	Stephania japonica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11351	Stephania japonica	Species	Menispermaceae	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

Activity Type	# Activity
IC50	1
Others	2

Activity Type	# Activity
Individual Protein	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT271	Individual Protein	Delta opioid receptor	Homo sapiens	IC50	=	2100.0	nM	PMID[20426456]
NPT145	Individual Protein	Mu opioid receptor	Homo sapiens	Inhibition	=	68.0	%	PMID[20426456]
NPT272	Individual Protein	Kappa opioid receptor	Homo sapiens	Inhibition	=	0.0	%	PMID[20426456]

☑ 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 NPC488038 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	353
0.1-0.2	1429
0.2-0.3	4277
0.3-0.4	11207
0.4-0.5	8376
0.5-0.6	12027
0.6-0.7	4339
0.7-0.8	636
0.8-0.85	45
0.85-0.9	3
0.9-0.95	3
0.95-1	2

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 NPC488038 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	211
0.1-0.2	659
0.2-0.3	1222
0.3-0.4	2704
0.4-0.5	2362
0.5-0.6	1449
0.6-0.7	454
0.7-0.8	73
0.8-0.85	16
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