NPASS Natural Product

Natural Product: NPC324516

Natural Product ID:	NPC324516
Common Name:	[(2R,3S,5R)-3-Hydroxy-5-(5-Methyl-2,4-Dioxopyrimidin-1-Yl)Oxolan-2-Yl]Methyl Phosphono Hydrogen Phosphate
IUPAC Name:	[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen phosphate
Synonyms:
Molecular Formula:	C10H16N2O11P2
Standard InCHIKey:	UJLXYODCHAELLY-XLPZGREQSA-N
Standard InCHI:	InChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Canonical SMILES:	O[C@H]1C[C@@H](O[C@@H]1COP(=O)(OP(=O)(O)O)O)n1cc(C)c(nc1=O)O
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO1797	Homo sapiens	Species	Hominidae	Eukaryota	PMID[20065942]
NPO20338	Mus musculus	Species	Muridae	Eukaryota	PMID[19425150]
NPO730	Escherichia coli	Species	Enterobacteriaceae	Bacteria	PMID[21988831]

Biological Activity

Activity Type	# Activity
Others	15

Activity Type	# Activity
Individual Protein	6
Others	9

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		Activity	=	2700	nmol/min/mg	17353236
NPT2	Others	Unspecified		Activity	=	1100	nmol	17353236
NPT2	Others	Unspecified		Activity	=	260000	%	17353236
NPT2	Others	Unspecified		Activity	=	21	nmol/min/mg	17353236
NPT2	Others	Unspecified		Activity	=	2	nmol	17353236
NPT2	Others	Unspecified		Activity	=	490	%	17353236
NPT6109	Individual Protein	Nucleoside diphosphate kinase 1	Homo sapiens	Activity	=	1.3	nM	17353236
NPT6109	Individual Protein	Nucleoside diphosphate kinase 1	Homo sapiens	Activity	=	89000	%	17353236
NPT6110	Individual Protein	Nucleoside diphosphate kinase 2	Homo sapiens	Activity	=	1.4	nM	17353236
NPT6110	Individual Protein	Nucleoside diphosphate kinase 2	Homo sapiens	Activity	=	1000	nmol	17353236
NPT6110	Individual Protein	Nucleoside diphosphate kinase 2	Homo sapiens	Activity	=	83000	%	17353236
NPT6109	Individual Protein	Nucleoside diphosphate kinase 1	Homo sapiens	Activity	=	1000	nmol	17353236
NPT2	Others	Unspecified		Activity	=	137	nmol/min/mg	17353236
NPT2	Others	Unspecified		Activity	=	0.049	nmol	17353236
NPT2	Others	Unspecified		Activity	=	1300	%	17353236

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 NPC324516 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	49
0.1-0.2	2736
0.2-0.3	21359
0.3-0.4	5981
0.4-0.5	682
0.5-0.6	38
0.6-0.7	14
0.7-0.8	13
0.8-0.85	4
0.85-0.9	11
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC318166
0.9767	High Similarity	NPC327344
0.8953	High Similarity	NPC71339
0.8953	High Similarity	NPC112842
0.8889	High Similarity	NPC320249
0.8889	High Similarity	NPC322594
0.8778	High Similarity	NPC324390
0.8667	High Similarity	NPC171116
0.8652	High Similarity	NPC163352
0.8652	High Similarity	NPC210456
0.8602	High Similarity	NPC73765
0.8602	High Similarity	NPC317639
0.8602	High Similarity	NPC283698
0.8495	Intermediate Similarity	NPC36985
0.8495	Intermediate Similarity	NPC17892
0.8427	Intermediate Similarity	NPC325723
0.8	Intermediate Similarity	NPC106780
0.7941	Intermediate Similarity	NPC329277
0.7788	Intermediate Similarity	NPC155087
0.7788	Intermediate Similarity	NPC149843
0.7742	Intermediate Similarity	NPC43246
0.7742	Intermediate Similarity	NPC89051
0.764	Intermediate Similarity	NPC325902
0.7374	Intermediate Similarity	NPC329384
0.7184	Intermediate Similarity	NPC328914
0.7157	Intermediate Similarity	NPC328779
0.7143	Intermediate Similarity	NPC315063
0.7143	Intermediate Similarity	NPC329077
0.7059	Intermediate Similarity	NPC120887
0.7041	Intermediate Similarity	NPC328806
0.6961	Remote Similarity	NPC280946
0.6961	Remote Similarity	NPC6166
0.6961	Remote Similarity	NPC226769
0.6807	Remote Similarity	NPC284651
0.6771	Remote Similarity	NPC319753
0.6731	Remote Similarity	NPC90240
0.6465	Remote Similarity	NPC229249
0.6435	Remote Similarity	NPC478024
0.6275	Remote Similarity	NPC62927
0.6275	Remote Similarity	NPC190334
0.6179	Remote Similarity	NPC325750
0.6105	Remote Similarity	NPC315806
0.608	Remote Similarity	NPC315058
0.6	Remote Similarity	NPC109188
0.5938	Remote Similarity	NPC313962

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC324516 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	55
0.1-0.2	817
0.2-0.3	6167
0.3-0.4	1758
0.4-0.5	255
0.5-0.6	36
0.6-0.7	36
0.7-0.8	23
0.8-0.85	7
0.85-0.9	7
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8953	High Similarity	NPD280	Approved
0.875	High Similarity	NPD240	Phase 3
0.8667	High Similarity	NPD841	Approved
0.8602	High Similarity	NPD9639	Clinical (unspecified phase)
0.8526	High Similarity	NPD5789	Clinical (unspecified phase)
0.8523	High Similarity	NPD239	Phase 2
0.8523	High Similarity	NPD238	Clinical (unspecified phase)
0.8333	Intermediate Similarity	NPD170	Approved
0.8261	Intermediate Similarity	NPD755	Phase 3
0.8182	Intermediate Similarity	NPD9556	Approved
0.809	Intermediate Similarity	NPD9560	Approved
0.809	Intermediate Similarity	NPD9561	Approved
0.8085	Intermediate Similarity	NPD251	Approved
0.8	Intermediate Similarity	NPD9546	Phase 2
0.7941	Intermediate Similarity	NPD3129	Phase 3
0.7917	Intermediate Similarity	NPD501	Phase 1
0.7912	Intermediate Similarity	NPD9533	Phase 2
0.7843	Intermediate Similarity	NPD3128	Phase 3
0.7826	Intermediate Similarity	NPD9557	Clinical (unspecified phase)
0.7802	Intermediate Similarity	NPD9559	Phase 1
0.7778	Intermediate Similarity	NPD9558	Phase 3
0.7742	Intermediate Similarity	NPD9580	Clinical (unspecified phase)
0.7742	Intermediate Similarity	NPD9562	Discovery
0.7742	Intermediate Similarity	NPD9581	Clinical (unspecified phase)
0.7677	Intermediate Similarity	NPD502	Approved
0.7609	Intermediate Similarity	NPD9529	Phase 1
0.75	Intermediate Similarity	NPD7914	Suspended
0.7387	Intermediate Similarity	NPD7992	Clinical (unspecified phase)
0.7297	Intermediate Similarity	NPD3139	Phase 3
0.7292	Intermediate Similarity	NPD241	Discontinued
0.7273	Intermediate Similarity	NPD1686	Approved
0.7245	Intermediate Similarity	NPD9565	Discontinued
0.7207	Intermediate Similarity	NPD3138	Phase 3
0.7184	Intermediate Similarity	NPD1454	Phase 3
0.7184	Intermediate Similarity	NPD1455	Phase 3
0.7113	Intermediate Similarity	NPD1760	Approved
0.7059	Intermediate Similarity	NPD762	Discontinued
0.6944	Remote Similarity	NPD1385	Discontinued
0.687	Remote Similarity	NPD7756	Clinical (unspecified phase)
0.6822	Remote Similarity	NPD1061	Clinical (unspecified phase)
0.6733	Remote Similarity	NPD500	Discontinued
0.6697	Remote Similarity	NPD6946	Approved
0.6598	Remote Similarity	NPD9573	Phase 2
0.6542	Remote Similarity	NPD223	Clinical (unspecified phase)
0.6505	Remote Similarity	NPD285	Discontinued
0.6465	Remote Similarity	NPD205	Approved
0.6465	Remote Similarity	NPD9601	Approved
0.6462	Remote Similarity	NPD7761	Suspended
0.6449	Remote Similarity	NPD192	Phase 2
0.6429	Remote Similarity	NPD2691	Clinical (unspecified phase)
0.6408	Remote Similarity	NPD267	Discontinued
0.64	Remote Similarity	NPD9555	Phase 2
0.6364	Remote Similarity	NPD9503	Approved
0.6364	Remote Similarity	NPD9504	Approved
0.6346	Remote Similarity	NPD6943	Clinical (unspecified phase)
0.6275	Remote Similarity	NPD9604	Approved
0.6275	Remote Similarity	NPD9603	Phase 3
0.6275	Remote Similarity	NPD9602	Phase 3
0.6239	Remote Similarity	NPD765	Discontinued
0.6214	Remote Similarity	NPD301	Discontinued
0.6214	Remote Similarity	NPD9553	Approved
0.6214	Remote Similarity	NPD9554	Approved
0.6162	Remote Similarity	NPD9600	Approved
0.6161	Remote Similarity	NPD2633	Phase 1
0.6126	Remote Similarity	NPD7651	Approved
0.6105	Remote Similarity	NPD9653	Clinical (unspecified phase)
0.6075	Remote Similarity	NPD1706	Clinical (unspecified phase)
0.6075	Remote Similarity	NPD215	Discontinued
0.6058	Remote Similarity	NPD723	Phase 2
0.604	Remote Similarity	NPD9572	Clinical (unspecified phase)
0.6038	Remote Similarity	NPD9585	Discontinued
0.6	Remote Similarity	NPD1331	Approved
0.6	Remote Similarity	NPD9405	Approved
0.5981	Remote Similarity	NPD279	Clinical (unspecified phase)
0.5963	Remote Similarity	NPD514	Clinical (unspecified phase)
0.5948	Remote Similarity	NPD6693	Phase 3
0.5913	Remote Similarity	NPD1428	Phase 2
0.59	Remote Similarity	NPD9429	Discontinued
0.5856	Remote Similarity	NPD3121	Phase 2
0.5816	Remote Similarity	NPD9407	Approved
0.5763	Remote Similarity	NPD284	Phase 1
0.5739	Remote Similarity	NPD4743	Phase 2
0.5727	Remote Similarity	NPD6948	Phase 3
0.5714	Remote Similarity	NPD1805	Phase 2
0.5714	Remote Similarity	NPD1804	Phase 2
0.5667	Remote Similarity	NPD4521	Clinical (unspecified phase)

Structure

CID324516 OpenBabel06191716172D 25 26 0 0 1 0 0 0 0 0999 V2000 -5.4478 -6.5306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0388 -2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7433 -4.9483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5523 -5.5361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0878 -2.0570 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5000 -2.8660 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0388 -3.3660 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4659 -5.1294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7614 -3.5471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5704 -4.1349 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.8479 -3.9538 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.7788 -1.1060 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2749 -5.7172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8659 -2.5526 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0878 -3.6750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 P 0 0 3 0 0 0 0 0 0 0 0 0 1 5 1 0 0 0 0 2 6 1 0 0 0 0 3 5 2 0 0 0 0 3 12 1 0 0 0 0 4 21 1 0 0 0 0 5 9 1 0 0 0 0 6 7 1 0 0 0 0 6 13 1 6 0 0 0 7 4 1 1 0 0 0 7 22 1 0 0 0 0 8 2 1 1 0 0 0 8 12 1 0 0 0 0 8 22 1 0 0 0 0 9 11 2 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 10 15 2 0 0 0 0 16 24 1 0 0 0 0 17 24 1 0 0 0 0 18 24 2 0 0 0 0 19 25 1 0 0 0 0 20 25 2 0 0 0 0 21 25 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	164628
ChEMBL	CHEMBL259724
ZINC

Physicochemical Properties

Molecular Weight:	402.02
ALogP:	-1.9863
MLogP:	0.91
XLogP:	-3.887
# Rotatable Bonds:	12
Polar Surface Area:	215.27
# H-Bond Aceptor:	13
# H-Bond Donor:	5
# Rings:	2
# Heavy Atoms:	25

Download Data

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Structure MOL file
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Biological Activities
Similar NPs/Drugs