NPASS Natural Product

Natural Product: NPC58001

Natural Product ID:	NPC58001
Common Name:	Virginiamycin Factor M1
IUPAC Name:
Synonyms:	Virginiamycin Factor M1; Virginiamycin M1
Molecular Formula:	C28H35N3O7
Standard InCHIKey:	DAIKHDNSXMZDCU-FQTGFAPKSA-N
Standard InCHI:	InChI=1S/C28H35N3O7/c1-17(2)26-19(4)9-10-24(34)29-11-5-7-18(3)13-20(32)14-21(33)15-25-30-22(16-37-25)27(35)31-12-6-8-23(31)28(36)38-26/h5,7-10,13,16-17,19-20,26,32H,6,11-12,14-15H2,1-4H3,(H,29,34)/b7-5+,10-9+,18-13+/t19-,20-,26-/m1/s1
Canonical SMILES:	OC1=NC/C=C/C(=C/[C@@H](O)CC(=O)Cc2nc(C(=O)N3C(=CCC3)C(=O)O[C@@H]([C@@H](/C=C/1)C)C(C)C)co2)/C
First Find Year:
Max Developmental Stage:
Synthetic Gene Cluster:	;

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Reference
NPO30193	Mycoplasma genitalium	Species	Mycoplasmataceae	Bacteria	PMID[22817898]
NPO8948	Streptomyces pristinaespiralis	Species	Streptomycetaceae	Bacteria	PMID[25708513]
NPO9874	Gueriniella serratulae	Species	Monophlebidae	Eukaryota	UNPD*
NPO7227	Nepeta tuberosa	Species	Lamiaceae	Eukaryota	UNPD*
NPO3349	Cryptosporiopsis abietina	Species	Dermateaceae	Eukaryota	UNPD*
NPO10141	Alstonia lenormandii	Species	Apocynaceae	Eukaryota	UNPD*
NPO184	Halobates hayanus	Species	Gerridae	Eukaryota	UNPD*
NPO7663	Carex pendula	Species	Cyperaceae	Eukaryota	UNPD*
NPO2225	Neonauclea sessilifolia	Species	Rubiaceae	Eukaryota	UNPD*
NPO3157	Polysyncraton echinatum	Species	Didemnidae	Eukaryota	UNPD*
NPO9360	Hydrangea macrophylla	Species	Hydrangeaceae	Eukaryota	UNPD*

Biological Activity

Activity Type	# Activity
MIC	13

Activity Type	# Activity
Organism	13

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	128	ug/ml	19047652
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	4	ug/ml	19047652
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	128	ug/ml	19047652
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	4	ug/ml	19470508
NPT1101	Organism	Staphylococcus aureus subsp. aureus RN4220	Staphylococcus aureus subsp. aureus RN4220	MIC	=	32	ug/ml	19470508
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	32	ug/ml	20921317
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	1	ug/ml	20921317

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 NPC58001 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	160
0.1-0.2	1224
0.2-0.3	6055
0.3-0.4	18177
0.4-0.5	4731
0.5-0.6	498
0.6-0.7	23
0.7-0.8	20
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC314523
0.7656	Intermediate Similarity	NPC476829
0.764	Intermediate Similarity	NPC30527
0.7458	Intermediate Similarity	NPC211555
0.7452	Intermediate Similarity	NPC325683
0.744	Intermediate Similarity	NPC477219
0.7404	Intermediate Similarity	NPC37924
0.7401	Intermediate Similarity	NPC186452
0.7368	Intermediate Similarity	NPC476828
0.7311	Intermediate Similarity	NPC322800
0.7311	Intermediate Similarity	NPC477218
0.7311	Intermediate Similarity	NPC168135
0.7273	Intermediate Similarity	NPC476830
0.7264	Intermediate Similarity	NPC177432
0.7264	Intermediate Similarity	NPC299035
0.7238	Intermediate Similarity	NPC12660
0.7225	Intermediate Similarity	NPC476826
0.7225	Intermediate Similarity	NPC476827
0.7225	Intermediate Similarity	NPC476831
0.7204	Intermediate Similarity	NPC476832
0.7198	Intermediate Similarity	NPC54983
0.6866	Remote Similarity	NPC224395
0.6866	Remote Similarity	NPC208297
0.6816	Remote Similarity	NPC107458
0.6816	Remote Similarity	NPC295653
0.6748	Remote Similarity	NPC258022
0.67	Remote Similarity	NPC58112
0.67	Remote Similarity	NPC306300
0.67	Remote Similarity	NPC88938
0.665	Remote Similarity	NPC103452
0.665	Remote Similarity	NPC199461
0.665	Remote Similarity	NPC46313
0.6585	Remote Similarity	NPC289029
0.6585	Remote Similarity	NPC48323
0.6512	Remote Similarity	NPC309919
0.6504	Remote Similarity	NPC477586
0.6504	Remote Similarity	NPC477590
0.6504	Remote Similarity	NPC477588
0.6504	Remote Similarity	NPC477585
0.6443	Remote Similarity	NPC475455
0.6416	Remote Similarity	NPC477587
0.6416	Remote Similarity	NPC477589
0.621	Remote Similarity	NPC49195
0.6023	Remote Similarity	NPC120335
0.5876	Remote Similarity	NPC237219
0.5781	Remote Similarity	NPC50274
0.5753	Remote Similarity	NPC316403
0.5739	Remote Similarity	NPC309525
0.5721	Remote Similarity	NPC220408
0.5676	Remote Similarity	NPC314222
0.5676	Remote Similarity	NPC196449
0.5645	Remote Similarity	NPC472436
0.5636	Remote Similarity	NPC472287
0.5636	Remote Similarity	NPC472286
0.5625	Remote Similarity	NPC119481
0.5619	Remote Similarity	NPC475342
0.5617	Remote Similarity	NPC475196
0.5615	Remote Similarity	NPC165964
0.5614	Remote Similarity	NPC313804
0.5614	Remote Similarity	NPC315804
0.5607	Remote Similarity	NPC59827
0.5607	Remote Similarity	NPC184933
0.5605	Remote Similarity	NPC476514
0.5602	Remote Similarity	NPC316224

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC58001 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	130
0.1-0.2	456
0.2-0.3	1602
0.3-0.4	3978
0.4-0.5	2735
0.5-0.6	252
0.6-0.7	7
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8626	High Similarity	NPD7896	Approved
0.6502	Remote Similarity	NPD6347	Phase 2
0.639	Remote Similarity	NPD7490	Discontinued
0.625	Remote Similarity	NPD6857	Phase 3
0.6227	Remote Similarity	NPD7180	Phase 3
0.6109	Remote Similarity	NPD6974	Phase 3
0.6096	Remote Similarity	NPD7031	Phase 1
0.6	Remote Similarity	NPD7547	Clinical (unspecified phase)
0.5973	Remote Similarity	NPD2433	Clinical (unspecified phase)
0.5939	Remote Similarity	NPD4898	Clinical (unspecified phase)
0.588	Remote Similarity	NPD7853	Phase 2
0.5856	Remote Similarity	NPD4667	Clinical (unspecified phase)
0.5844	Remote Similarity	NPD7284	Clinical (unspecified phase)
0.5823	Remote Similarity	NPD7022	Phase 2
0.5813	Remote Similarity	NPD2957	Phase 2
0.5808	Remote Similarity	NPD3263	Phase 3
0.5804	Remote Similarity	NPD5443	Clinical (unspecified phase)
0.5801	Remote Similarity	NPD1659	Phase 1
0.5787	Remote Similarity	NPD4368	Phase 2
0.5785	Remote Similarity	NPD1638	Discovery
0.5763	Remote Similarity	NPD4394	Clinical (unspecified phase)
0.5748	Remote Similarity	NPD772	Phase 3
0.5739	Remote Similarity	NPD5640	Discontinued
0.5721	Remote Similarity	NPD7811	Phase 3
0.5721	Remote Similarity	NPD7810	Phase 3
0.5714	Remote Similarity	NPD2779	Approved
0.5696	Remote Similarity	NPD6247	Clinical (unspecified phase)
0.567	Remote Similarity	NPD3945	Discontinued
0.5669	Remote Similarity	NPD5922	Phase 3
0.5636	Remote Similarity	NPD2951	Discontinued
0.5625	Remote Similarity	NPD5866	Approved
0.5622	Remote Similarity	NPD8104	Phase 3
0.5605	Remote Similarity	NPD3392	Approved

Structure

CID58001 OpenBabel06191715392D 38 40 0 0 1 0 0 0 0 0999 V2000 0.3520 -2.4496 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9663 -1.3262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6420 2.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0889 -2.1930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4784 0.7406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1078 2.5195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7041 1.7148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5961 1.6603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4646 -1.5767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4644 -1.5995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9982 -0.1366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4489 3.2717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3452 3.6634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0261 5.1419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1309 5.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2794 4.1201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0172 -1.5073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6586 2.7138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5081 -1.2851 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.7873 4.4933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1182 5.5611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4215 4.6155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6209 1.8816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4332 -1.3517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1374 5.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6657 -0.7462 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1737 3.8118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4397 0.8981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2992 -0.8517 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.2113 5.2287 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.5299 2.8774 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.5335 5.1590 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4099 6.5176 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8106 -2.2777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0509 4.2920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3894 0.5848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1374 4.6155 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 17 1 0 0 0 0 2 17 1 0 0 0 0 3 18 1 0 0 0 0 5 7 2 0 0 0 0 5 11 1 0 0 0 0 6 8 1 0 0 0 0 6 12 1 0 0 0 0 7 18 1 0 0 0 0 8 23 2 0 0 0 0 9 10 2 0 0 0 0 9 19 1 0 0 0 0 10 24 1 0 0 0 0 11 29 1 0 0 0 0 12 31 1 0 0 0 0 13 18 2 0 0 0 0 13 20 1 0 0 0 0 14 20 1 0 0 0 0 14 21 1 0 0 0 0 15 21 1 0 0 0 0 15 25 1 0 0 0 0 16 22 2 0 0 0 0 16 37 1 0 0 0 0 19 4 1 1 0 0 0 19 26 1 0 0 0 0 20 32 1 6 0 0 0 21 33 2 0 0 0 0 22 27 1 0 0 0 0 22 30 1 0 0 0 0 23 28 1 0 0 0 0 23 31 1 0 0 0 0 24 29 2 3 0 0 0 24 34 1 0 0 0 0 25 30 2 0 0 0 0 25 37 1 0 0 0 0 26 17 1 1 0 0 0 26 38 1 0 0 0 0 27 31 1 0 0 0 0 27 35 2 0 0 0 0 28 36 2 0 0 0 0 28 38 1 0 0 0 0 M END $$$$

External Identifiers

PubChem CID	5459319
ChEMBL	CHEMBL1236670
ZINC

Physicochemical Properties

Molecular Weight:	525.25
ALogP:	0.2645
MLogP:	3.44
XLogP:	1.586
# Rotatable Bonds:	7
Polar Surface Area:	142.53
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	38

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