NPASS Compound

Structure

CID241935 OpenBabel06191716042D 53 61 0 0 1 0 0 0 0 0999 V2000 -6.5027 0.5248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1099 -0.7876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7342 2.5096 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2428 0.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6012 -1.3022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1786 -2.6421 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3815 -2.1900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9995 0.5692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0464 1.7889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0470 1.6869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0852 0.5206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8007 0.5480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7898 -0.7996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7891 -1.2843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4065 1.4751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7966 0.1171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2062 -0.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3470 1.6570 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6903 1.3825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9918 -0.8318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8109 1.1172 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9986 0.0850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6071 1.0997 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3477 1.2241 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8077 1.4644 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5383 1.2820 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9811 -2.1788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5794 -2.6531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0063 1.4860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3942 -0.2623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7484 0.6732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1631 0.2682 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9531 -0.4124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4190 -0.0691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0971 -1.8275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2558 -0.7022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1291 1.6788 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4409 0.5092 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6102 1.9277 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4802 0.5726 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6858 -2.5889 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5824 -3.4685 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7124 1.8937 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1236 -1.3163 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2319 -0.4994 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5033 -2.5244 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3353 -1.4070 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3163 2.3354 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0008 -1.9991 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9873 -1.2629 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7821 -2.2006 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2089 1.9384 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 1 16 1 0 0 0 0 2 17 1 0 0 0 0 5 49 1 0 0 0 0 6 7 1 0 0 0 0 6 27 1 0 0 0 0 7 28 1 0 0 0 0 8 16 2 0 0 0 0 8 29 1 0 0 0 0 9 21 1 0 0 0 0 10 19 1 0 0 0 0 10 26 1 0 0 0 0 11 23 1 0 0 0 0 11 24 1 0 0 0 0 12 22 1 0 0 0 0 12 25 1 0 0 0 0 13 16 1 0 0 0 0 13 50 1 0 0 0 0 14 20 1 0 0 0 0 14 51 1 0 0 0 0 15 39 1 0 0 0 0 15 52 1 0 0 0 0 17 30 2 0 0 0 0 17 35 1 0 0 0 0 18 9 1 1 0 0 0 18 19 1 0 0 0 0 18 21 1 0 0 0 0 19 31 2 0 0 0 0 20 22 2 0 0 0 0 20 36 1 0 0 0 0 21 38 1 1 0 0 0 23 24 1 0 0 0 0 23 37 1 6 0 0 0 24 39 1 6 0 0 0 25 37 1 1 0 0 0 25 39 1 0 0 0 0 26 37 1 6 0 0 0 26 40 1 0 0 0 0 27 41 2 0 0 0 0 27 50 1 0 0 0 0 28 42 2 0 0 0 0 28 51 1 0 0 0 0 29 43 2 0 0 0 0 29 52 1 0 0 0 0 30 32 1 0 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 31 38 1 0 0 0 0 32 40 1 6 0 0 0 33 34 1 0 0 0 0 33 44 2 0 0 0 0 34 38 1 1 0 0 0 34 45 1 0 0 0 0 35 46 2 0 0 0 0 35 49 1 0 0 0 0 36 47 2 0 0 0 0 36 53 1 0 0 0 0 37 3 1 6 0 0 0 38 4 1 1 0 0 0 39 48 1 6 0 0 0 40 22 1 6 0 0 0 40 53 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	732.28
Volume:	711.296
LogP:	3.472
LogD:	2.775
LogS:	-4.873
# Rotatable Bonds:	2
TPSA:	185.87
# H-Bond Aceptor:	13
# H-Bond Donor:	1
# Rings:	9
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.18
Synthetic Accessibility Score:	7.938
Fsp3:	0.675
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.174
MDCK Permeability:	8.92301177373156e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.565
Human Intestinal Absorption (HIA):	0.049
20% Bioavailability (F20%):	0.968
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.281
Plasma Protein Binding (PPB):	72.09136962890625%
Volume Distribution (VD):	0.419
Pgp-substrate:	13.025246620178223%

ADMET: Metabolism

CYP1A2-inhibitor:	0.036
CYP1A2-substrate:	0.695
CYP2C19-inhibitor:	0.848
CYP2C19-substrate:	0.233
CYP2C9-inhibitor:	0.932
CYP2C9-substrate:	0.011
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.027
CYP3A4-inhibitor:	0.927
CYP3A4-substrate:	0.749

ADMET: Excretion

Clearance (CL):	6.108
Half-life (T1/2):	0.122

ADMET: Toxicity

hERG Blockers:	0.299
Human Hepatotoxicity (H-HT):	0.088
Drug-inuced Liver Injury (DILI):	0.491
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.161
Maximum Recommended Daily Dose:	0.962
Skin Sensitization:	0.463
Carcinogencity:	0.118
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.924

Download Data

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

Natural Product: NPC241935

Natural Product ID:	NPC241935
*Common Name:**	Shizukaol F
IUPAC Name:	n.a.
Synonyms:	Shizukaol F
Standard InCHIKey:	XOCHXEVAPBOSPH-RCNNXFIWSA-N
Standard InCHI:	InChI=1S/C40H44O13/c1-16-8-29(43)52-15-39(48)24-11-23(24)37(3)25(39)12-22-20(14-51-28(42)7-6-27(41)50-13-16)36(47)53-40(22)26(37)10-19-18-9-21(18)38(4)31(19)32(40)30(33(44)34(38)45)17(2)35(46)49-5/h8,18,21,23-26,32,34,45,48H,6-7,9-15H2,1-5H3/b16-8+,30-17-/t18-,21-,23-,24+,25-,26+,32+,34+,37+,38+,39+,40+/m1/s1
SMILES:	COC(=O)/C(=C/1C(=O)[C@H](O)[C@@]2(C3=C(C[C@@H]4[C@@]5([C@@H]13)OC(=O)C1=C5C[C@@H]3[C@]4(C)[C@@H]4C[C@@H]4[C@@]3(O)COC(=O)/C=C(C)/COC(=O)CCC(=O)OC1)[C@@H]1[C@H]2C1)C)/C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1813268
PubChem CID:	56681897
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[9542132]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30724564]
NPO11257	Momordica dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30673219]
NPO15190	Chloranthus fortunei	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27997206]
NPO21178	Chloranthus serratus	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27588583]
NPO17386	Securidaca longepedunculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24216090]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[2413754]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[23394984]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	Germany		PMID[23394984]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	New Zealand		PMID[23394984]

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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	4
IC50	4
Others	4

Activity Type	# Activity
Cell Line	5
Organism	5
Others	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	Activity	=	53.1	%	PMID[491879]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	50000.0	nM	PMID[491879]
NPT1374	Cell Line	WI-38	Homo sapiens	IC50	=	230.0	nM	PMID[491878]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	11.0	nM	PMID[491878]
NPT2	Others	Unspecified	""	Ratio IC50	=	21.0	n.a.	PMID[491878]
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	=	21040.0	nM	PMID[491877]
NPT1452	Cell Line	C8166	Homo sapiens	CC50	=	47.0	nM	PMID[491876]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	110.0	nM	PMID[491876]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	3390.0	nM	PMID[491876]
NPT24	Organism	Human immunodeficiency virus 1	Human immunodeficiency virus 1	EC50	=	4050.0	nM	PMID[491876]

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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 NPC241935 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	300
0.1-0.2	1673
0.2-0.3	4891
0.3-0.4	8558
0.4-0.5	12338
0.5-0.6	7061
0.6-0.7	5826
0.7-0.8	1872
0.8-0.85	133
0.85-0.9	18
0.9-0.95	4
0.95-1	23

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC279478
0.9917	High Similarity	NPC34963
0.9835	High Similarity	NPC58029
0.9835	High Similarity	NPC469673
0.9754	High Similarity	NPC476823

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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 NPC241935 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	252
0.1-0.2	1877
0.2-0.3	3905
0.3-0.4	2028
0.4-0.5	614
0.5-0.6	240
0.6-0.7	154
0.7-0.8	78
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.808	Intermediate Similarity	NPD7115	Discovery
0.8031	Intermediate Similarity	NPD6319	Approved
0.7955	Intermediate Similarity	NPD7319	Approved
0.7951	Intermediate Similarity	NPD6372	Approved
0.7951	Intermediate Similarity	NPD6373	Approved

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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