NPASS Compound

Structure

NPC475762 OpenBabel07101719152D 30 30 0 0 1 0 0 0 0 0999 V2000 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 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 -0.8660 0.5000 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 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 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 O 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 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 -0.8660 -2.5000 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 6 1 0 0 0 0 2 11 1 0 0 0 0 3 12 1 0 0 0 0 4 13 1 0 0 0 0 5 14 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 9 10 2 0 0 0 0 9 16 1 0 0 0 0 10 17 1 0 0 0 0 11 21 2 0 0 0 0 11 26 1 0 0 0 0 12 22 2 0 0 0 0 12 27 1 0 0 0 0 13 23 2 0 0 0 0 13 28 1 0 0 0 0 14 24 2 0 0 0 0 14 29 1 0 0 0 0 15 8 1 1 0 0 0 15 18 1 0 0 0 0 15 26 1 0 0 0 0 16 19 1 0 0 0 0 16 27 1 6 0 0 0 17 25 2 0 0 0 0 17 30 1 0 0 0 0 18 20 1 0 0 0 0 18 28 1 6 0 0 0 19 20 1 6 0 0 0 19 30 1 0 0 0 0 20 29 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	428.17
Volume:	418.003
LogP:	2.028
LogD:	1.179
LogS:	-2.798
# Rotatable Bonds:	14
TPSA:	131.5
# H-Bond Aceptor:	10
# H-Bond Donor:	0
# Rings:	1
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.371
Synthetic Accessibility Score:	4.328
Fsp3:	0.65
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:	-4.998
MDCK Permeability:	0.00012100345338694751
Pgp-inhibitor:	0.988
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.961
20% Bioavailability (F20%):	0.598
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.544
Plasma Protein Binding (PPB):	30.65326690673828%
Volume Distribution (VD):	1.351
Pgp-substrate:	36.76231002807617%

ADMET: Metabolism

CYP1A2-inhibitor:	0.178
CYP1A2-substrate:	0.016
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.01
CYP2C9-substrate:	0.029
CYP2D6-inhibitor:	0.972
CYP2D6-substrate:	0.054
CYP3A4-inhibitor:	0.277
CYP3A4-substrate:	0.16

ADMET: Excretion

Clearance (CL):	2.345
Half-life (T1/2):	0.912

ADMET: Toxicity

hERG Blockers:	0.064
Human Hepatotoxicity (H-HT):	0.976
Drug-inuced Liver Injury (DILI):	0.909
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.219
Maximum Recommended Daily Dose:	0.214
Skin Sensitization:	0.84
Carcinogencity:	0.047
Eye Corrosion:	0.028
Eye Irritation:	0.038
Respiratory Toxicity:	0.274

Download Data

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

Natural Product: NPC475762

Natural Product ID:	NPC475762
*Common Name:**	[(2R,3S)-6-Oxo-2-[(1S,2R,3S)-1,2,3-Triacetyloxyheptyl]-2,3-Dihydropyran-3-Yl] Acetate
IUPAC Name:	[(2R,3S)-6-oxo-2-[(1S,2R,3S)-1,2,3-triacetyloxyheptyl]-2,3-dihydropyran-3-yl] acetate
Synonyms:
Standard InCHIKey:	MORVXKHVGBWREP-UFHDJZAFSA-N
Standard InCHI:	InChI=1S/C20H28O10/c1-6-7-8-15(26-11(2)21)18(28-13(4)23)20(29-14(5)24)19-16(27-12(3)22)9-10-17(25)30-19/h9-10,15-16,18-20H,6-8H2,1-5H3/t15-,16-,18+,19+,20-/m0/s1
SMILES:	CCCC[C@@H]([C@H]([C@@H]([C@H]1[C@H](C=CC(=O)O1)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL514889
PubChem CID:	10387847
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

*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
NPO28865	Hyptis pectinata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8496706]
NPO40549	Hyptis pectinata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30601004]
NPO28865	Hyptis pectinata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28865	Hyptis pectinata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO28865	Hyptis pectinata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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
ED50	11
IC50	3
MIC	5
Others	2

Activity Type	# Activity
Cell Line	10
NON-MOLECULAR	4
Organism	7

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT148	Cell Line	HCT-15	Homo sapiens	IC50	>	10000.0	nM	PMID[506756]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	2700.0	nM	PMID[506756]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	7700.0	nM	PMID[506756]
NPT453	Cell Line	HT-1080	Homo sapiens	ED50	=	8.4	ug ml-1	PMID[506755]
NPT147	Cell Line	SK-MEL-2	Homo sapiens	ED50	=	4.5	ug ml-1	PMID[506755]
NPT91	Cell Line	KB	Homo sapiens	ED50	=	4.4	ug ml-1	PMID[506755]
NPT168	Cell Line	P388	Mus musculus	ED50	=	0.4	ug ml-1	PMID[506755]
NPT762	Cell Line	A-431	Homo sapiens	ED50	=	2.6	ug ml-1	PMID[506755]
NPT858	Cell Line	LNCaP	Homo sapiens	ED50	=	1.9	ug ml-1	PMID[506755]
NPT133	Cell Line	ZR-75-1	Homo sapiens	ED50	=	7.8	ug ml-1	PMID[506755]

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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 NPC475762 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	199
0.1-0.2	2296
0.2-0.3	6776
0.3-0.4	17970
0.4-0.5	9889
0.5-0.6	4111
0.6-0.7	1294
0.7-0.8	130
0.8-0.85	15
0.85-0.9	10
0.9-0.95	5
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9545	High Similarity	NPC475760
0.9296	High Similarity	NPC474026
0.9041	High Similarity	NPC473947
0.9041	High Similarity	NPC180725
0.8939	High Similarity	NPC25747

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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 NPC475762 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	169
0.1-0.2	2829
0.2-0.3	3770
0.3-0.4	1877
0.4-0.5	394
0.5-0.6	100
0.6-0.7	10
0.7-0.8	1
0.8-0.85	0
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
0.7442	Intermediate Similarity	NPD7838	Discovery
0.7241	Intermediate Similarity	NPD46	Approved
0.7241	Intermediate Similarity	NPD6698	Approved
0.6882	Remote Similarity	NPD8029	Clinical (unspecified phase)
0.6809	Remote Similarity	NPD6648	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