NPASS Compound

Structure

NPC483038 OpenBabel06302216182D 39 41 0 0 1 0 0 0 0 0999 V2000 0.8660 -2.5000 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 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 -0.8660 0.5000 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 -0.0000 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 3.5000 0.0000 C 0 0 1 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 -2.5981 3.5000 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 -4.3301 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 4.5000 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 -0.0000 5.0000 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 0.5000 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 1.7321 -1.0000 0.0000 O 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 3.4641 0.0000 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 4.3301 1.5000 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 O 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 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 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 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 39 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 36 1 0 0 0 0 6 7 1 0 0 0 0 7 33 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 8 35 1 0 0 0 0 9 10 1 0 0 0 0 9 20 1 0 0 0 0 11 10 1 1 0 0 0 11 12 1 0 0 0 0 11 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 14 16 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 20 30 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 33 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 32 1 0 0 0 0 28 29 1 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 33 34 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	532.28
Volume:	577.395
LogP:	8.054
LogD:	3.946
LogS:	-3.521
# Rotatable Bonds:	10
TPSA:	111.13
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.12
Synthetic Accessibility Score:	4.413
Fsp3:	0.364
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.062
MDCK Permeability:	1.1935716429434251e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.985
Human Intestinal Absorption (HIA):	0.522
20% Bioavailability (F20%):	0.944
30% Bioavailability (F30%):	0.153

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	95.0810317993164%
Volume Distribution (VD):	0.728
Pgp-substrate:	7.215359687805176%

ADMET: Metabolism

CYP1A2-inhibitor:	0.184
CYP1A2-substrate:	0.228
CYP2C19-inhibitor:	0.564
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.647
CYP2C9-substrate:	0.885
CYP2D6-inhibitor:	0.141
CYP2D6-substrate:	0.189
CYP3A4-inhibitor:	0.084
CYP3A4-substrate:	0.08

ADMET: Excretion

Clearance (CL):	5.009
Half-life (T1/2):	0.149

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.989
Drug-inuced Liver Injury (DILI):	0.975
AMES Toxicity:	0.047
Rat Oral Acute Toxicity:	0.816
Maximum Recommended Daily Dose:	0.888
Skin Sensitization:	0.68
Carcinogencity:	0.165
Eye Corrosion:	0.003
Eye Irritation:	0.841
Respiratory Toxicity:	0.385

Download Data

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

Natural Product: NPC483038

Natural Product ID:	NPC483038
*Common Name:**	BYXLSGOQQDBGNL-FGZHOGPDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BYXLSGOQQDBGNL-FGZHOGPDSA-N
Standard InCHI:	InChI=1S/C33H40O6/c1-17(2)9-11-21(19(5)6)15-24-28(35)25(16-22(20(7)8)12-10-18(3)4)32-27(30(24)37)29(36)23-13-14-26(34)31(38)33(23)39-32/h9-10,13-14,21-22,34-35,37-38H,5,7,11-12,15-16H2,1-4,6,8H3/t21-,22-/m1/s1
SMILES:	CC(=CC[C@H](Cc1c(c(C[C@@H](CC=C(C)C)C(=C)C)c2c(c(=O)c3ccc(c(c3o2)O)O)c1O)O)C(=C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	132937453
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003518] 4-prenylated xanthones

*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
NPO32997	Hypericum monogynum	Species	Hypericaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[25924023]
NPO32997	Hypericum monogynum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27525351]

☑ 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	4

Activity Type	# Activity
Cell Line	1
NON-MOLECULAR	1
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT34	Cell Line	BV-2	Mus musculus	IC50	=	7470.0	nM	PMID[27525351]
NPT610	Others	Molecular identity unknown		Activity	=	91.97	%	PMID[27525351]
NPT610	Others	Molecular identity unknown		Activity	=	83.77	%	PMID[27525351]
NPT610	Others	Molecular identity unknown		Activity	=	78.42	%	PMID[27525351]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Activity	>	90.0	%	PMID[27525351]

☑ 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 NPC483038 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	446
0.1-0.2	1750
0.2-0.3	4399
0.3-0.4	10755
0.4-0.5	7239
0.5-0.6	3711
0.6-0.7	5185
0.7-0.8	4941
0.8-0.85	2394
0.85-0.9	1275
0.9-0.95	540
0.95-1	62

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 NPC483038 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	398
0.1-0.2	973
0.2-0.3	1730
0.3-0.4	2708
0.4-0.5	1809
0.5-0.6	982
0.6-0.7	381
0.7-0.8	114
0.8-0.85	38
0.85-0.9	10
0.9-0.95	7
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