NPASS Compound

Structure

CID312763 OpenBabel06191716122D 36 40 0 0 1 0 0 0 0 0999 V2000 -0.3275 6.8380 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7143 4.7342 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9156 5.1941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2343 5.1941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6973 -1.1717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4527 -1.1717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0830 6.2582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1445 2.4419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0054 2.4419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0906 0.1490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9407 0.1490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9587 5.3140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5512 4.3143 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5988 4.3143 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2246 2.6884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9254 2.6884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3910 1.5220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2411 1.5220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5512 2.0150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5988 2.0150 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2246 3.6408 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9254 3.6408 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.7176 0.8486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4324 0.8486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7977 1.0951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3523 1.0951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0788 4.9495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1045 4.0053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6767 5.5293 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4508 -0.2518 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6992 -0.2518 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2396 1.0896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0896 1.0896 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1500 0.0000 0.0000 O 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 0.0455 4.0053 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 7 1 0 0 0 0 2 12 1 0 0 0 0 5 30 1 0 0 0 0 6 31 1 0 0 0 0 7 12 2 0 0 0 0 8 15 2 0 0 0 0 8 17 1 0 0 0 0 9 16 2 0 0 0 0 9 18 1 0 0 0 0 10 32 1 0 0 0 0 10 34 1 0 0 0 0 11 33 1 0 0 0 0 11 35 1 0 0 0 0 12 27 1 0 0 0 0 13 3 1 1 0 0 0 13 14 1 0 0 0 0 13 21 1 0 0 0 0 14 4 1 1 0 0 0 14 22 1 0 0 0 0 15 19 1 0 0 0 0 15 21 1 0 0 0 0 16 20 1 0 0 0 0 16 22 1 0 0 0 0 17 23 2 0 0 0 0 17 32 1 0 0 0 0 18 24 2 0 0 0 0 18 33 1 0 0 0 0 19 20 1 0 0 0 0 19 25 2 0 0 0 0 20 26 2 0 0 0 0 21 28 1 6 0 0 0 22 36 1 1 0 0 0 23 25 1 0 0 0 0 23 34 1 0 0 0 0 24 26 1 0 0 0 0 24 35 1 0 0 0 0 25 30 1 0 0 0 0 26 31 1 0 0 0 0 27 29 2 0 0 0 0 27 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	498.19
Volume:	490.786
LogP:	3.854
LogD:	3.819
LogS:	-4.603
# Rotatable Bonds:	5
TPSA:	101.91
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.475
Synthetic Accessibility Score:	4.399
Fsp3:	0.444
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:	-4.76
MDCK Permeability:	4.0693648770684376e-05
Pgp-inhibitor:	0.979
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.002
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.025

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.041
Plasma Protein Binding (PPB):	81.66565704345703%
Volume Distribution (VD):	1.219
Pgp-substrate:	11.42461109161377%

ADMET: Metabolism

CYP1A2-inhibitor:	0.161
CYP1A2-substrate:	0.938
CYP2C19-inhibitor:	0.975
CYP2C19-substrate:	0.897
CYP2C9-inhibitor:	0.908
CYP2C9-substrate:	0.857
CYP2D6-inhibitor:	0.655
CYP2D6-substrate:	0.341
CYP3A4-inhibitor:	0.958
CYP3A4-substrate:	0.801

ADMET: Excretion

Clearance (CL):	11.842
Half-life (T1/2):	0.086

ADMET: Toxicity

hERG Blockers:	0.077
Human Hepatotoxicity (H-HT):	0.13
Drug-inuced Liver Injury (DILI):	0.735
AMES Toxicity:	0.035
Rat Oral Acute Toxicity:	0.046
Maximum Recommended Daily Dose:	0.206
Skin Sensitization:	0.052
Carcinogencity:	0.557
Eye Corrosion:	0.003
Eye Irritation:	0.088
Respiratory Toxicity:	0.669

Download Data

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

Natural Product: NPC312763

Natural Product ID:	NPC312763
*Common Name:**	Schisantherin L
IUPAC Name:	n.a.
Synonyms:	Schisantherin L
Standard InCHIKey:	JTLHKPZZCOQRTA-LYFNIGRZSA-N
Standard InCHI:	InChI=1S/C27H30O9/c1-7-12(2)27(29)36-22-14(4)13(3)21(28)15-8-17-23(34-10-32-17)25(30-5)19(15)20-16(22)9-18-24(26(20)31-6)35-11-33-18/h7-9,13-14,21-22,28H,10-11H2,1-6H3/b12-7-/t13-,14+,21+,22+/m1/s1
SMILES:	C/C=C(C(=O)O[C@H]1[C@@H](C)[C@@H](C)[C@H](O)c2c(c3c1cc1OCOc1c3OC)c(OC)c1c(c2)OCO1)/C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL465719
PubChem CID:	44567624
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
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	Stems	n.a.	n.a.	PMID[27704807]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26214125]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24299567]
NPO18146	Kadsura angustifolia	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21232955]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18590312]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	roots	n.a.	n.a.	PMID[18491866]
NPO18146	Kadsura angustifolia	Species	Schisandraceae	Eukaryota	stems	Honghe Prefecture of Yunnan Province, China	2005-Oct	PMID[18278869]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18271558]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18027905]
NPO912	Kadsura coccinea	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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
Others	2

Activity Type	# Activity
Cell Line	1
Organism	1
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1452	Cell Line	C8166	Homo sapiens	CC50	>	200000.0	nM	PMID[451883]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	137970.0	nM	PMID[451883]
NPT2	Others	Unspecified	""	Ratio	=	2.91	n.a.	PMID[451883]

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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 NPC312763 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	331
0.1-0.2	1433
0.2-0.3	3526
0.3-0.4	8448
0.4-0.5	10184
0.5-0.6	4077
0.6-0.7	7468
0.7-0.8	6479
0.8-0.85	551
0.85-0.9	130
0.9-0.95	61
0.95-1	9

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Similarity Score	Similarity Level	Natural Product ID
0.9796	High Similarity	NPC24562
0.973	High Similarity	NPC198461
0.9726	High Similarity	NPC473989
0.9658	High Similarity	NPC85141
0.96	High Similarity	NPC473323

Showing 1 to 5 of 200 entries

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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 NPC312763 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	277
0.1-0.2	886
0.2-0.3	1798
0.3-0.4	2771
0.4-0.5	1801
0.5-0.6	986
0.6-0.7	530
0.7-0.8	94
0.8-0.85	3
0.85-0.9	4
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8968	High Similarity	NPD4966	Approved
0.8968	High Similarity	NPD4967	Phase 2
0.8968	High Similarity	NPD4965	Approved
0.8774	High Similarity	NPD37	Approved
0.8734	High Similarity	NPD6234	Discontinued

Showing 1 to 5 of 200 entries

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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