NPASS Compound

Structure

NPC471748 OpenBabel07101718282D 43 47 0 0 1 0 0 0 0 0999 V2000 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 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 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -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 -3.4641 -2.0000 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 -2.5981 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 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 -3.4641 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 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 -3.4641 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 -2.5981 -1.5000 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 -2.5981 2.5000 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 -4.3301 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 -5.1962 -3.0000 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 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 3 2 0 0 0 0 2 9 1 0 0 0 0 3 11 1 0 0 0 0 4 9 2 0 0 0 0 4 12 1 0 0 0 0 5 10 2 0 0 0 0 5 13 1 0 0 0 0 6 10 1 0 0 0 0 6 14 2 0 0 0 0 7 28 1 0 0 0 0 8 1 1 6 0 0 0 8 23 1 0 0 0 0 8 39 1 0 0 0 0 9 24 1 0 0 0 0 10 29 1 0 0 0 0 11 12 2 0 0 0 0 11 30 1 0 0 0 0 12 31 1 0 0 0 0 13 16 2 0 0 0 0 13 32 1 0 0 0 0 14 16 1 0 0 0 0 14 40 1 0 0 0 0 15 7 1 1 0 0 0 15 17 1 0 0 0 0 15 41 1 0 0 0 0 16 18 1 0 0 0 0 17 19 1 0 0 0 0 17 33 1 1 0 0 0 18 25 1 0 0 0 0 18 34 2 0 0 0 0 19 21 1 0 0 0 0 19 35 1 6 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 20 36 1 6 0 0 0 21 27 1 0 0 0 0 21 37 1 6 0 0 0 22 26 1 0 0 0 0 22 38 1 6 0 0 0 23 42 1 1 0 0 0 24 25 2 0 0 0 0 24 40 1 0 0 0 0 25 43 1 0 0 0 0 26 39 1 0 0 0 0 26 43 1 1 0 0 0 27 41 1 0 0 0 0 27 42 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	610.15
Volume:	552.318
LogP:	0.244
LogD:	-0.185
LogS:	-3.747
# Rotatable Bonds:	6
TPSA:	269.43
# H-Bond Aceptor:	16
# H-Bond Donor:	10
# Rings:	5
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.14
Synthetic Accessibility Score:	4.776
Fsp3:	0.444
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.462
MDCK Permeability:	2.4776481950539164e-05
Pgp-inhibitor:	0.01
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.848
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.043
Plasma Protein Binding (PPB):	86.4303207397461%
Volume Distribution (VD):	0.691
Pgp-substrate:	16.27431297302246%

ADMET: Metabolism

CYP1A2-inhibitor:	0.131
CYP1A2-substrate:	0.03
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.129
CYP2D6-inhibitor:	0.033
CYP2D6-substrate:	0.142
CYP3A4-inhibitor:	0.057
CYP3A4-substrate:	0.004

ADMET: Excretion

Clearance (CL):	1.525
Half-life (T1/2):	0.747

ADMET: Toxicity

hERG Blockers:	0.251
Human Hepatotoxicity (H-HT):	0.122
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.852
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.924
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.203
Respiratory Toxicity:	0.024

Download Data

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

Natural Product: NPC471748

Natural Product ID:	NPC471748
*Common Name:**	3-[(2S,3R,4S,5R,6S)-3,4-Dihydroxy-6-Methyl-5-[(2S,3R,4R,5R,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxyoxan-2-Yl]Oxy-2-(3,4-Dihydroxyphenyl)-5,7-Dihydroxychromen-4-One
IUPAC Name:	3-[(2S,3R,4S,5R,6S)-3,4-dihydroxy-6-methyl-5-[(2S,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-2-(3,4-dihydroxyphenyl)-5,7-dihydroxychromen-4-one
Synonyms:
Standard InCHIKey:	CAENGMLSMONNBU-UPUYEFMOSA-N
Standard InCHI:	InChI=1S/C27H30O16/c1-8-23(42-27-21(37)19(35)17(33)15(7-28)41-27)20(36)22(38)26(39-8)43-25-18(34)16-13(32)5-10(29)6-14(16)40-24(25)9-2-3-11(30)12(31)4-9/h2-6,8,15,17,19-23,26-33,35-38H,7H2,1H3/t8-,15+,17-,19+,20-,21+,22+,23-,26-,27-/m0/s1
SMILES:	OC[C@H]1O[C@@H](O[C@H]2[C@H](C)O[C@H]([C@@H]([C@@H]2O)O)Oc2c(oc3c(c2=O)c(O)cc(c3)O)c2ccc(c(c2)O)O)[C@@H]([C@@H]([C@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL311088
PubChem CID:	44460538
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003531] Flavonoid-3-O-glycosides

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO33513	hydrangeae dulcis folium	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9871657]
NPO33513	hydrangeae dulcis folium	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[11549443]

Showing 1 to 2 of 2 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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
Others	5

Activity Type	# Activity
Cell Line	1
Organism	4

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1178	Cell Line	KB 3-1	Homo sapiens	Cytotoxicity	=	2.1	ug ml-1	PMID[464304]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Activity	=	48.1	ng ml-1	PMID[464304]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Activity	=	43.4	ng ml-1	PMID[464304]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Activity	=	32.8	ng ml-1	PMID[464304]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Activity	=	25.0	ng ml-1	PMID[464304]

Showing 1 to 5 of 5 entries

Previous1Next

☑ 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 NPC471748 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	460
0.1-0.2	1842
0.2-0.3	4252
0.3-0.4	9791
0.4-0.5	8319
0.5-0.6	4578
0.6-0.7	5577
0.7-0.8	5191
0.8-0.85	1537
0.85-0.9	565
0.9-0.95	424
0.95-1	161

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC155877
1.0	High Similarity	NPC134532
1.0	High Similarity	NPC33054
1.0	High Similarity	NPC203259
1.0	High Similarity	NPC176740

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC471748 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	404
0.1-0.2	953
0.2-0.3	1998
0.3-0.4	2741
0.4-0.5	1793
0.5-0.6	852
0.6-0.7	273
0.7-0.8	104
0.8-0.85	18
0.85-0.9	6
0.9-0.95	2
0.95-1	6

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD6797	Phase 2
0.9938	High Similarity	NPD7251	Discontinued
0.9755	High Similarity	NPD7808	Phase 3
0.9691	High Similarity	NPD7472	Approved
0.963	High Similarity	NPD7054	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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