NPASS Compound

Structure

CID102256 OpenBabel06191715442D 31 33 0 0 1 0 0 0 0 0999 V2000 1.5477 -4.0581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5040 -3.7610 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1631 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7322 0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4964 1.3988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4881 1.8215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3415 2.2441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0894 2.2441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8536 -2.5203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7643 -1.3334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3334 -1.3334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4227 -2.5203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1869 -3.1870 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8536 -1.5774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4227 -1.5774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0083 -0.4227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5774 -0.4227 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1869 -0.9107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2440 -0.9107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3416 0.2440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9107 0.2440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4309 0.0000 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 0.2440 -3.1870 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3671 -4.1218 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9191 -0.1786 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4882 -0.1786 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5857 1.1548 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1548 1.1548 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0975 1.3334 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3334 1.3334 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 3 26 1 0 0 0 0 4 27 1 0 0 0 0 5 28 1 0 0 0 0 6 29 1 0 0 0 0 7 30 1 0 0 0 0 8 31 1 0 0 0 0 9 13 1 0 0 0 0 9 14 1 0 0 0 0 10 14 2 0 0 0 0 10 16 1 0 0 0 0 11 15 2 0 0 0 0 11 17 1 0 0 0 0 12 15 1 0 0 0 0 12 24 1 0 0 0 0 13 24 1 6 0 0 0 14 18 1 0 0 0 0 15 19 1 0 0 0 0 16 20 2 0 0 0 0 16 26 1 0 0 0 0 17 21 2 0 0 0 0 17 27 1 0 0 0 0 18 19 1 0 0 0 0 18 22 2 0 0 0 0 19 23 2 0 0 0 0 20 22 1 0 0 0 0 20 28 1 0 0 0 0 21 23 1 0 0 0 0 21 29 1 0 0 0 0 22 30 1 0 0 0 0 23 31 1 0 0 0 0 24 2 1 6 0 0 0 24 25 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	432.21
Volume:	443.704
LogP:	3.112
LogD:	3.131
LogS:	-3.439
# Rotatable Bonds:	6
TPSA:	75.61
# H-Bond Aceptor:	7
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.742
Synthetic Accessibility Score:	3.444
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
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:	-4.7
MDCK Permeability:	2.8004447813145816e-05
Pgp-inhibitor:	0.967
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.093

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.054
Plasma Protein Binding (PPB):	65.71683502197266%
Volume Distribution (VD):	0.639
Pgp-substrate:	34.39697265625%

ADMET: Metabolism

CYP1A2-inhibitor:	0.075
CYP1A2-substrate:	0.988
CYP2C19-inhibitor:	0.13
CYP2C19-substrate:	0.931
CYP2C9-inhibitor:	0.043
CYP2C9-substrate:	0.859
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.914
CYP3A4-inhibitor:	0.625
CYP3A4-substrate:	0.872

ADMET: Excretion

Clearance (CL):	6.298
Half-life (T1/2):	0.137

ADMET: Toxicity

hERG Blockers:	0.365
Human Hepatotoxicity (H-HT):	0.06
Drug-inuced Liver Injury (DILI):	0.155
AMES Toxicity:	0.063
Rat Oral Acute Toxicity:	0.203
Maximum Recommended Daily Dose:	0.041
Skin Sensitization:	0.196
Carcinogencity:	0.044
Eye Corrosion:	0.003
Eye Irritation:	0.044
Respiratory Toxicity:	0.035

Download Data

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

Natural Product: NPC102256

Natural Product ID:	NPC102256
*Common Name:**	Schizandrin
IUPAC Name:	n.a.
Synonyms:	Schisandrin
Standard InCHIKey:	YEFOAORQXAOVJQ-RZFZLAGVSA-N
Standard InCHI:	InChI=1S/C24H32O7/c1-13-9-14-10-16(26-3)20(28-5)22(30-7)18(14)19-15(12-24(13,2)25)11-17(27-4)21(29-6)23(19)31-8/h10-11,13,25H,9,12H2,1-8H3/t13-,24-/m0/s1
SMILES:	COc1c(OC)cc2c(c1OC)c1c(cc(c(c1OC)OC)OC)C[C@@H]([C@@](C2)(C)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL253688
PubChem CID:	3001664
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

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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[25302569]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24959987]
NPO8187	Schisandra chinensis	Species	Schisandraceae	Eukaryota	n.a.	fruit	n.a.	PMID[24155209]
NPO29191	Schisandra neglecta	Species	Schisandraceae	Eukaryota	Stems	Luoji Mountain Village, Xichang County, Sicuan Province, China	2011-Sep	PMID[23738539]
NPO7385	Schisandra sphenanthera	Species	Schisandraceae	Eukaryota	fruits	n.a.	n.a.	PMID[23265871]
NPO33401	schisandra sphenathera	Species	Schisandraceae	Eukaryota	stems	n.a.	n.a.	PMID[23237974]
NPO8210	Trigonella foenum-graecum	Species	Fabaceae	Eukaryota	n.a.	seed	n.a.	PMID[21381697]
NPO18146	Kadsura angustifolia	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21232955]
NPO24804	Schisandra rubriflora	Species	Schisandraceae	Eukaryota	leaves and stems	n.a.	n.a.	PMID[20146529]
NPO18146	Kadsura angustifolia	Species	Schisandraceae	Eukaryota	stems	Honghe Prefecture of Yunnan Province, China	2005-Oct	PMID[18278869]

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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
EC50	1
IC50	28
Others	10
Potency	5

Activity Type	# Activity
Cell Line	20
CELL-LINE	1
Individual Protein	9
NON-MOLECULAR	2
Organism	4
Others	7
PROTEIN COMPLEX	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	=	8500.0	nM	PMID[506915]
NPT90	Cell Line	DU-145	Homo sapiens	IC50	=	5380.0	nM	PMID[506915]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	5060.0	nM	PMID[506915]
NPT71	Cell Line	HEK293	Homo sapiens	IC50	=	80470.0	nM	PMID[506915]
NPT2	Others	Unspecified		IC50	=	5360.0	nM	PMID[506915]
NPT2	Others	Unspecified		Ratio IC50	=	3.8	n.a.	PMID[506914]
NPT71	Cell Line	HEK293	Homo sapiens	IC50	=	81740.0	nM	PMID[506913]
NPT90	Cell Line	DU-145	Homo sapiens	IC50	=	13090.0	nM	PMID[506913]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	32560.0	nM	PMID[506913]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	21650.0	nM	PMID[506913]

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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 NPC102256 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	406
0.1-0.2	1676
0.2-0.3	4425
0.3-0.4	12705
0.4-0.5	5668
0.5-0.6	4235
0.6-0.7	8299
0.7-0.8	3995
0.8-0.85	809
0.85-0.9	405
0.9-0.95	53
0.95-1	21

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Similarity Score	Similarity Level	Natural Product ID
0.968	High Similarity	NPC207702
0.968	High Similarity	NPC149008
0.968	High Similarity	NPC283114
0.9612	High Similarity	NPC180602
0.9612	High Similarity	NPC214853

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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 NPC102256 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	356
0.1-0.2	955
0.2-0.3	1796
0.3-0.4	2789
0.4-0.5	1625
0.5-0.6	921
0.6-0.7	584
0.7-0.8	115
0.8-0.85	8
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8571	High Similarity	NPD3027	Phase 3
0.8284	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.8284	Intermediate Similarity	NPD3018	Phase 2
0.8254	Intermediate Similarity	NPD5283	Phase 1
0.8222	Intermediate Similarity	NPD1529	Clinical (unspecified phase)

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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