NPASS Natural Product

Natural Product: NPC103409

Natural Product ID:	NPC103409
Common Name:	Skimmin
IUPAC Name:	7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-2-one
Synonyms:	Skimmin
Molecular Formula:	C15H16O8
Standard InCHIKey:	VPAOSFFTKWUGAD-TVKJYDDYSA-N
Standard InCHI:	InChI=1S/C15H16O8/c16-6-10-12(18)13(19)14(20)15(23-10)21-8-3-1-7-2-4-11(17)22-9(7)5-8/h1-5,10,12-16,18-20H,6H2/t10-,12-,13+,14-,15-/m1/s1
Canonical SMILES:	OC[C@H]1O[C@@H](Oc2ccc3c(c2)oc(=O)cc3)[C@@H]([C@H]([C@@H]1O)O)O
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	Eukaryota	UNPD*
NPO10211	Pajanelia multijuga	NA	NA	NA	UNPD*
NPO1109	Corydalis persica	Species	Papaveraceae	Eukaryota	UNPD*
NPO11430	Inula grantioides	Species	Asteraceae	Eukaryota	UNPD*
NPO12339	Daphne feddei	Species	Thymelaeaceae	Eukaryota	UNPD*
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	UNPD*
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	UNPD*
NPO13647	Calcarisporium thermophilum	Species	NA	Eukaryota	UNPD*
NPO13848	Amomum daniellii	Species	Zingiberaceae	Eukaryota	UNPD*
NPO14526	Plectranthus caninus	Species	Lamiaceae	Eukaryota	UNPD*

Showing 1 to 10 of 31 entries

Previous1 2 3 4Next

Biological Activity

Activity Type	# Activity
IC50	1
Others	9

Activity Type	# Activity
Organism	9
Others	1

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	GI	=	0	%	22901896
NPT1198	Organism	Magnaporthe grisea	Magnaporthe grisea	IZ	=	0	mm	22901896
NPT1493	Organism	Ceratocystis paradoxa	Ceratocystis paradoxa	GI	=	5.8	%	22901896
NPT1493	Organism	Ceratocystis paradoxa	Ceratocystis paradoxa	IZ	=	1.5	mm	22901896
NPT1494	Organism	Alternaria mali	Alternaria mali	GI	=	0	%	22901896
NPT1494	Organism	Alternaria mali	Alternaria mali	IZ	=	0	mm	22901896
NPT2	Others	Unspecified		GI	=	15.3	%	22901896
NPT722	Organism	Athelia rolfsii	Athelia rolfsii	GI	=	24.1	%	22901896
NPT722	Organism	Athelia rolfsii	Athelia rolfsii	IZ	=	2.8	mm	22901896
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	4150000	nM	18675491

Showing 1 to 10 of 10 entries

Previous1Next

Similar Natural Products 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 NPC103409 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	243
0.1-0.2	1065
0.2-0.3	2879
0.3-0.4	6645
0.4-0.5	6296
0.5-0.6	3615
0.6-0.7	5044
0.7-0.8	4409
0.8-0.85	554
0.85-0.9	115
0.9-0.95	22
0.95-1	2

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.8392	Intermediate Similarity	NPC472353
0.8392	Intermediate Similarity	NPC475084
0.8397	Intermediate Similarity	NPC247553
0.8403	Intermediate Similarity	NPC471028
0.8403	Intermediate Similarity	NPC297342

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC103409 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	233
0.1-0.2	812
0.2-0.3	1766
0.3-0.4	2822
0.4-0.5	1830
0.5-0.6	1104
0.6-0.7	458
0.7-0.8	129
0.8-0.85	4
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6712	Remote Similarity	NPD1481	Phase 2
0.6727	Remote Similarity	NPD4288	Approved
0.6728	Remote Similarity	NPD7458	Discontinued
0.6728	Remote Similarity	NPD5808	Clinical (unspecified phase)
0.6733	Remote Similarity	NPD3180	Approved

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

Structure

CID103409 OpenBabel06191715452D 23 25 0 0 1 0 0 0 0 0999 V2000 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 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 0.8660 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 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 -3.4641 -1.0000 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 -5.1962 -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 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 0.8660 -1.5000 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 1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -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 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 -0.8660 -1.5000 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 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 7 1 0 0 0 0 2 4 2 0 0 0 0 2 7 1 0 0 0 0 3 8 1 0 0 0 0 4 11 1 0 0 0 0 5 8 2 0 0 0 0 5 9 1 0 0 0 0 6 16 1 0 0 0 0 7 9 2 0 0 0 0 8 21 1 0 0 0 0 9 22 1 0 0 0 0 10 6 1 6 0 0 0 10 12 1 0 0 0 0 10 23 1 0 0 0 0 11 17 2 0 0 0 0 11 22 1 0 0 0 0 12 13 1 0 0 0 0 12 18 1 1 0 0 0 13 14 1 0 0 0 0 13 19 1 6 0 0 0 14 15 1 0 0 0 0 14 20 1 1 0 0 0 15 21 1 6 0 0 0 15 23 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	99693
ChEMBL	CHEMBL526377
ZINC

Physicochemical Properties

Molecular Weight:	324.08
ALogP:	-1.9372
MLogP:	2.23
XLogP:	0.424
# Rotatable Bonds:	7
Polar Surface Area:	125.68
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	3
# Heavy Atoms:	23

Download Data

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