NPASS Natural Product

Natural Product: NPC104712

Natural Product ID:	NPC104712
Common Name:	Lynamicin B
IUPAC Name:	methyl 3-(5-chloro-1H-indol-3-yl)-4-(5,6-dichloro-1H-indol-3-yl)-1H-pyrrole-2-carboxylate
Synonyms:
Molecular Formula:	C22H14Cl3N3O2
Standard InCHIKey:	HJXJUNZGSRTQEN-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C22H14Cl3N3O2/c1-30-22(29)21-20(14-8-26-18-3-2-10(23)4-11(14)18)15(9-28-21)13-7-27-19-6-17(25)16(24)5-12(13)19/h2-9,26-28H,1H3
Canonical SMILES:	COC(=O)c1[nH]cc(c1c1c[nH]c2c1cc(Cl)cc2)c1c[nH]c2c1cc(Cl)c(c2)Cl
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO31745	Streptomyces scsio 03032	Species	Streptomycetaceae	Bacteria				StreptomeDB*
NPO33622	actinomycete sp. NPS12745	Species	NA	NA	isolated from a marine sediment sample	Mission Bay, San Diego, CA		PMID[18842058]

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Biological Activity

Activity Type	# Activity
IC50	1
MIC	11

Activity Type	# Activity
Organism	12

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1118	Organism	Streptococcus pneumoniae	Streptococcus pneumoniae	MIC	=	18000	nM	18842058
NPT1122	Organism	Haemophilus influenzae	Haemophilus influenzae	MIC	=	4400	nM	18842058
NPT1122	Organism	Haemophilus influenzae	Haemophilus influenzae	MIC	=	13000	nM	18842058
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	4400	nM	18842058
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	1800	nM	18842058
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	2200	nM	18842058
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	2200	nM	18842058
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	3300	nM	18842058
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	13000	nM	18842058
NPT2665	Organism	unidentified herpesvirus	unidentified herpesvirus	IC50	=	17.2	ug/ml	18842058

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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 NPC104712 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	466
0.1-0.2	3341
0.2-0.3	9844
0.3-0.4	12790
0.4-0.5	2012
0.5-0.6	1444
0.6-0.7	923
0.7-0.8	61
0.8-0.85	2
0.85-0.9	1
0.9-0.95	4
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.6652	Remote Similarity	NPC308931
0.6652	Remote Similarity	NPC473189
0.6653	Remote Similarity	NPC221100
0.6653	Remote Similarity	NPC476287
0.6653	Remote Similarity	NPC119006

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Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC104712 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	278
0.1-0.2	727
0.2-0.3	1031
0.3-0.4	2005
0.4-0.5	2738
0.5-0.6	1873
0.6-0.7	471
0.7-0.8	38
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
0.6414	Remote Similarity	NPD2920	Discontinued
0.6414	Remote Similarity	NPD5022	Discontinued
0.6414	Remote Similarity	NPD7824	Approved
0.6417	Remote Similarity	NPD7704	Clinical (unspecified phase)
0.6417	Remote Similarity	NPD7853	Phase 2

Showing 1 to 5 of 200 entries

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Structure

CID104712 OpenBabel06191715452D 30 34 0 0 0 0 0 0 0 0999 V2000 3.4826 -0.4598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1759 4.8531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9190 4.1840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0169 3.5659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1261 2.3781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1261 4.3781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2788 3.3781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7111 1.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2248 4.5441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7601 2.8968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 2.8781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 2.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7601 1.8968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9921 2.8781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9921 3.8781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7111 3.2058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2601 3.8781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7601 -0.2788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4817 5.2132 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.8581 2.3781 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.8581 4.3781 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 3.2989 2.3968 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 4.1871 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6555 -1.2733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6736 0.1280 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 30 1 0 0 0 0 2 3 2 0 0 0 0 2 10 1 0 0 0 0 3 18 1 0 0 0 0 4 10 2 0 0 0 0 4 11 1 0 0 0 0 5 12 1 0 0 0 0 5 16 2 0 0 0 0 6 17 2 0 0 0 0 6 19 1 0 0 0 0 7 13 2 0 0 0 0 7 27 1 0 0 0 0 8 14 2 0 0 0 0 8 26 1 0 0 0 0 9 15 2 0 0 0 0 9 28 1 0 0 0 0 10 23 1 0 0 0 0 11 14 1 0 0 0 0 11 18 2 0 0 0 0 12 13 1 0 0 0 0 12 19 2 0 0 0 0 13 15 1 0 0 0 0 14 20 1 0 0 0 0 15 20 1 0 0 0 0 16 17 1 0 0 0 0 16 24 1 0 0 0 0 17 25 1 0 0 0 0 18 26 1 0 0 0 0 19 27 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 28 1 0 0 0 0 22 29 2 0 0 0 0 22 30 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	11271102
ChEMBL	CHEMBL489557
ZINC

Physicochemical Properties

Molecular Weight:	457.02
ALogP:	0.9829
MLogP:	3
XLogP:	3.87
# Rotatable Bonds:	8
Polar Surface Area:	73.67
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	30

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