NPASS Compound

Structure

NPC443873 OpenBabel06302216132D 26 27 0 0 0 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 0.8660 -1.5000 0.0000 O 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 -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 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 -2.5981 0.5000 0.0000 C 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 -3.4641 -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 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 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 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 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 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 24 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 1 0 0 0 0 6 23 2 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 16 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 21 1 0 0 0 0 14 15 2 0 0 0 0 14 19 1 0 0 0 0 15 16 1 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	358.14
Volume:	369.013
LogP:	2.969
LogD:	3.125
LogS:	-4.888
# Rotatable Bonds:	8
TPSA:	63.22
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.53
Synthetic Accessibility Score:	2.03
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.763
MDCK Permeability:	3.7954701838316396e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.976
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.166

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.2
Plasma Protein Binding (PPB):	77.39643859863281%
Volume Distribution (VD):	0.52
Pgp-substrate:	18.32798957824707%

ADMET: Metabolism

CYP1A2-inhibitor:	0.639
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.779
CYP2C19-substrate:	0.886
CYP2C9-inhibitor:	0.337
CYP2C9-substrate:	0.934
CYP2D6-inhibitor:	0.043
CYP2D6-substrate:	0.936
CYP3A4-inhibitor:	0.847
CYP3A4-substrate:	0.734

ADMET: Excretion

Clearance (CL):	9.314
Half-life (T1/2):	0.661

ADMET: Toxicity

hERG Blockers:	0.374
Human Hepatotoxicity (H-HT):	0.111
Drug-inuced Liver Injury (DILI):	0.842
AMES Toxicity:	0.233
Rat Oral Acute Toxicity:	0.068
Maximum Recommended Daily Dose:	0.043
Skin Sensitization:	0.836
Carcinogencity:	0.125
Eye Corrosion:	0.015
Eye Irritation:	0.369
Respiratory Toxicity:	0.781

Download Data

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

Natural Product: NPC443873

Natural Product ID:	NPC443873
*Common Name:**	MGRRLDUZDMYFMW-RMKNXTFCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MGRRLDUZDMYFMW-RMKNXTFCSA-N
Standard InCHI:	InChI=1S/C20H22O6/c1-22-14-7-8-15(17(12-14)23-2)16(21)9-6-13-10-18(24-3)20(26-5)19(11-13)25-4/h6-12H,1-5H3/b9-6+
SMILES:	COc1ccc(C(=O)/C=C/c2cc(c(c(c2)OC)OC)OC)c(c1)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6179330
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003467] Linear 1,3-diarylpropanoids

*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
NPO25653	Spatholobus suberectus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26690274]
NPO25653	Spatholobus suberectus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25653	Spatholobus suberectus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25653	Spatholobus suberectus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25653	Spatholobus suberectus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25653	Spatholobus suberectus	Species	Fabaceae	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	2
Others	9

Activity Type	# Activity
Cell Line	9
Others	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT369	Cell Line	ACHN	Homo sapiens	GI	=	79.0	%	PMID[20064725]
NPT461	Cell Line	PANC-1	Homo sapiens	GI	=	62.0	%	PMID[20064725]
NPT1307	Cell Line	Calu-1	Homo sapiens	GI	=	58.0	%	PMID[20064725]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI	=	57.0	%	PMID[20064725]
NPT393	Cell Line	HCT-116	Homo sapiens	GI	=	84.0	%	PMID[20064725]
NPT1970	Cell Line	THP-1	Homo sapiens	Inhibition	=	99.0	%	PMID[20064725]
NPT1970	Cell Line	THP-1	Homo sapiens	Inhibition	=	100.0	%	PMID[20064725]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	>	10000.0	nM	PMID[26690274]
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	6600.0	nM	PMID[26690274]
NPT1	Others	Radical scavenging activity		Activity	=	44.91	%	PMID[20064725]
NPT27	Others	Unspecified		Activity	=	39.0	%	PMID[20064725]

☑ 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 NPC443873 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	1766
0.2-0.3	5030
0.3-0.4	11958
0.4-0.5	5393
0.5-0.6	3752
0.6-0.7	5571
0.7-0.8	6163
0.8-0.85	2091
0.85-0.9	471
0.9-0.95	50
0.95-1	6

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 NPC443873 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	394
0.1-0.2	973
0.2-0.3	1673
0.3-0.4	2734
0.4-0.5	1722
0.5-0.6	1074
0.6-0.7	406
0.7-0.8	139
0.8-0.85	27
0.85-0.9	8
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