NPASS Compound

Structure

NPC485504 OpenBabel06302215582D 36 39 0 0 1 0 0 0 0 0999 V2000 8.5730 2.7688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6722 2.3956 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8987 2.9892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0260 3.9558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9979 2.6161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2244 3.2096 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8707 1.6494 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9699 1.2763 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2805 1.9657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7680 2.8101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2805 3.6545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3055 3.6545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8180 2.8101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3055 1.9657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6160 1.2763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6160 0.3013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3055 -0.3881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2805 -0.3881 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6536 -1.2889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9699 0.3013 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9365 0.4286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5634 -0.4722 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7717 -0.1862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9273 0.3013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9273 1.2763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7717 1.7638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7717 2.7388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.5776 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5731 0.7888 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 0.8680 2.8101 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3805 3.6545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8180 4.4988 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3055 5.3432 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7680 4.4988 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2805 5.3432 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 3 4 1 0 0 0 0 3 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 7 1 6 0 0 0 8 9 1 0 0 0 0 8 20 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 35 1 0 0 0 0 12 13 2 0 0 0 0 12 33 1 0 0 0 0 13 14 1 0 0 0 0 13 31 1 0 0 0 0 14 15 1 0 0 0 0 15 26 2 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 23 2 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 18 20 1 0 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 24 30 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 31 32 1 0 0 0 0 33 34 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	500.2
Volume:	499.343
LogP:	4.107
LogD:	3.194
LogS:	-4.469
# Rotatable Bonds:	6
TPSA:	112.91
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.458
Synthetic Accessibility Score:	4.193
Fsp3:	0.444
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.729
MDCK Permeability:	3.252594615332782e-05
Pgp-inhibitor:	0.984
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.032
Plasma Protein Binding (PPB):	85.3680648803711%
Volume Distribution (VD):	0.766
Pgp-substrate:	12.006117820739746%

ADMET: Metabolism

CYP1A2-inhibitor:	0.18
CYP1A2-substrate:	0.97
CYP2C19-inhibitor:	0.934
CYP2C19-substrate:	0.811
CYP2C9-inhibitor:	0.836
CYP2C9-substrate:	0.862
CYP2D6-inhibitor:	0.494
CYP2D6-substrate:	0.457
CYP3A4-inhibitor:	0.888
CYP3A4-substrate:	0.663

ADMET: Excretion

Clearance (CL):	10.121
Half-life (T1/2):	0.115

ADMET: Toxicity

hERG Blockers:	0.045
Human Hepatotoxicity (H-HT):	0.172
Drug-inuced Liver Injury (DILI):	0.433
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.438
Maximum Recommended Daily Dose:	0.364
Skin Sensitization:	0.293
Carcinogencity:	0.128
Eye Corrosion:	0.003
Eye Irritation:	0.462
Respiratory Toxicity:	0.869

Download Data

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

Natural Product: NPC485504

Natural Product ID:	NPC485504
*Common Name:**	BYZKFKFGPLUFIH-QHWVUYPCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BYZKFKFGPLUFIH-QHWVUYPCSA-N
Standard InCHI:	InChI=1S/C27H32O9/c1-8-13(2)26(29)36-25-16-11-17(31-5)23(32-6)24(33-7)20(16)19-15(9-14(3)27(25,4)30)10-18-22(21(19)28)35-12-34-18/h8,10-11,14,25,28,30H,9,12H2,1-7H3/b13-8+/t14-,25-,27-/m0/s1
SMILES:	C/C=C(C)/C(=O)O[C@H]1c2cc(c(c(c2-c2c(C[C@H](C)[C@]1(C)O)cc1c(c2O)OCO1)OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	45484581
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16562834]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	fruit	n.a.	PMID[24155209]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24959987]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25302569]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8187	Schisandra chinensis	Species	Schisandraceae	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	7
Others	28

Activity Type	# Activity
Cell Line	28
Organism	4
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT82	Cell Line	MDA-MB-231	Homo sapiens	IC50	=	33500.0	nM	PMID[18063366]
NPT1086	Cell Line	SK-HEP1	Homo sapiens	IC50	=	19900.0	nM	PMID[18063366]
NPT2548	Cell Line	SNU-638	Homo sapiens	IC50	=	15300.0	nM	PMID[18063366]
NPT396	Cell Line	T47D	Homo sapiens	IC50	=	26100.0	nM	PMID[18063366]
NPT148	Cell Line	HCT-15	Homo sapiens	IC50	=	5600.0	nM	PMID[18063366]
NPT111	Cell Line	K562	Homo sapiens	IC50	=	11300.0	nM	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	5600.0	nM	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	50.1	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	31.8	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	18.1	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	0.6	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	50.4	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	31.6	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	18.0	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	1.5	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	57.9	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	26.0	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	16.2	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	65.3	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	75.0	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	18.8	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	8.2	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	15.9	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	10.8	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	1.1	%	PMID[18063366]
NPT81	Cell Line	A549	Homo sapiens	Activity	=	2.5	%	PMID[18063366]
NPT71	Cell Line	HEK293	Homo sapiens	Inhibition	=	-9.3	%	PMID[24018191]
NPT27	Others	Unspecified		GI	>=	25.0	%	PMID[19640714]
NPT963	Organism	Hepatitis B virus	Hepatitis B virus	Inhibition	=	59.7	%	PMID[19640714]
NPT963	Organism	Hepatitis B virus	Hepatitis B virus	Inhibition	=	22.1	%	PMID[19640714]
NPT963	Organism	Hepatitis B virus	Hepatitis B virus	Inhibition	=	34.7	%	PMID[19640714]
NPT963	Organism	Hepatitis B virus	Hepatitis B virus	Inhibition	=	16.9	%	PMID[19640714]
NPT2	Others	Unspecified		Activity	=	201.0	%	PMID[25302569]

☑ 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 NPC485504 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	342
0.1-0.2	1470
0.2-0.3	3552
0.3-0.4	8537
0.4-0.5	9910
0.5-0.6	3960
0.6-0.7	6645
0.7-0.8	7052
0.8-0.85	977
0.85-0.9	172
0.9-0.95	58
0.95-1	22

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 NPC485504 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	290
0.1-0.2	901
0.2-0.3	1851
0.3-0.4	2760
0.4-0.5	1749
0.5-0.6	948
0.6-0.7	543
0.7-0.8	99
0.8-0.85	8
0.85-0.9	1
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