NP-MRD: Showing NP-Card for 2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid (NP0215595)

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Record Information

Version

2.0

Created at

2022-09-05 15:15:52 UTC

Updated at

2022-09-05 15:15:52 UTC

NP-MRD ID

NP0215595

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid

Description

Mildiomycin belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom. 2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid was first documented in 2008 (PMID: 18412191). Based on a literature review a small amount of articles have been published on Mildiomycin (PMID: 22753012) (PMID: 28000775) (PMID: 24920828) (PMID: 23659472).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052217152D          

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M  END

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M  END


  Mrv1652309052217152D          

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M  END
> <DATABASE_ID>
NP0215595

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CO)C(O)=N[C@H]1C=C[C@@H](O[C@@H]1C(O)(CC(O)CNC(N)=N)C(O)=O)N1C=C(CO)C(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C19H30N8O9/c20-10(7-29)15(31)25-11-1-2-12(27-5-8(6-28)14(21)26-18(27)34)36-13(11)19(35,16(32)33)3-9(30)4-24-17(22)23/h1-2,5,9-13,28-30,35H,3-4,6-7,20H2,(H,25,31)(H,32,33)(H2,21,26,34)(H4,22,23,24)/t9?,10?,11-,12+,13-,19?/m0/s1

> <INCHI_KEY>
QKJJCZYFXJCKRX-AMYGDCFASA-N

> <FORMULA>
C19H30N8O9

> <MOLECULAR_WEIGHT>
514.496

> <EXACT_MASS>
514.213574578

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
49.84465013619835

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S,3S,6R)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-imino-1,4-dihydropyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid

> <JCHEM_LOGP>
-8.329927980550316

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
3.4131304328215646

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.761418240474245

> <JCHEM_PKA_STRONGEST_BASIC>
11.384427886265648

> <JCHEM_POLAR_SURFACE_AREA>
307.64

> <JCHEM_REFRACTIVITY>
142.75240000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2S,3S,6R)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  N   UNK     0      -2.667   6.160   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334   5.390   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000   6.160   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0      -1.334   3.850   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334   0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.206  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       2.874  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.644  -2.104   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       3.644   0.564   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       8.002  -7.700   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0       5.335  -7.700   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0      -1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      -4.001  -5.390   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   11   14                                             
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    9   15   29                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   27                                                  
CONECT   17   16   18   25                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   17   26                                                  
CONECT   26   25                                                            
CONECT   27   16   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   14   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36                                                       
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₃₀N₈O₉

Average Mass

514.4960 Da

Monoisotopic Mass

514.21357 Da

IUPAC Name

2-[(2S,3S,6R)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-imino-1,4-dihydropyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid

Traditional Name

2-[(2S,3S,6R)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2H-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid

CAS Registry Number

Not Available

SMILES

NC(CO)C(O)=N[C@H]1C=C[C@@H](O[C@@H]1C(O)(CC(O)CNC(N)=N)C(O)=O)N1C=C(CO)C(=N)N=C1O

InChI Identifier

InChI=1S/C19H30N8O9/c20-10(7-29)15(31)25-11-1-2-12(27-5-8(6-28)14(21)26-18(27)34)36-13(11)19(35,16(32)33)3-9(30)4-24-17(22)23/h1-2,5,9-13,28-30,35H,3-4,6-7,20H2,(H,25,31)(H,32,33)(H2,21,26,34)(H4,22,23,24)/t9?,10?,11-,12+,13-,19?/m0/s1

InChI Key

QKJJCZYFXJCKRX-AMYGDCFASA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Gamma amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid amide
Serine or derivatives
Gamma amino acid or derivatives
Alpha-amino acid or derivatives
Aminopyrimidine
Pyrimidone
Alpha-hydroxy acid
Hydropyrimidine
Hydroxy acid
Pyran
Pyrimidine
Imidolactam
Heteroaromatic compound
Tertiary alcohol
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Amino acid
Guanidine
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Carboxylic acid
Monocarboxylic acid or derivatives
Aromatic alcohol
Organic oxygen compound
Organic nitrogen compound
Primary aliphatic amine
Organonitrogen compound
Organooxygen compound
Primary alcohol
Carbonyl group
Primary amine
Organic oxide
Alcohol
Amine
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-8.3	ChemAxon
pKa (Strongest Acidic)	2.76	ChemAxon
pKa (Strongest Basic)	11.38	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	307.64 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	142.75 m³·mol⁻¹	ChemAxon
Polarizability	49.84 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018185

Chemspider ID

8025063

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9849350

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wu J, Li L, Deng Z, Zabriskie TM, He X: Analysis of the mildiomycin biosynthesis gene cluster in Streptoverticillum remofaciens ZJU5119 and characterization of MilC, a hydroxymethyl cytosyl-glucuronic acid synthase. Chembiochem. 2012 Jul 23;13(11):1613-21. doi: 10.1002/cbic.201200173. Epub 2012 Jun 29. [PubMed:22753012 ]
Zhao G, Chen C, Xiong W, Gao T, Deng Z, Wu G, He X: Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis. Sci Rep. 2016 Dec 21;6:39675. doi: 10.1038/srep39675. [PubMed:28000775 ]
Zhao G, Wu G, Zhang Y, Liu G, Han T, Deng Z, He X: Structure of the N-glycosidase MilB in complex with hydroxymethyl CMP reveals its Arg23 specifically recognizes the substrate and controls its entry. Nucleic Acids Res. 2014 Jul;42(12):8115-24. doi: 10.1093/nar/gku486. Epub 2014 Jun 11. [PubMed:24920828 ]
Sikowitz MD, Cooper LE, Begley TP, Kaminski PA, Ealick SE: Reversal of the substrate specificity of CMP N-glycosidase to dCMP. Biochemistry. 2013 Jun 11;52(23):4037-47. doi: 10.1021/bi400316p. Epub 2013 May 28. [PubMed:23659472 ]
Li L, Xu Z, Xu X, Wu J, Zhang Y, He X, Zabriskie TM, Deng Z: The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5'-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. Chembiochem. 2008 May 23;9(8):1286-94. doi: 10.1002/cbic.200800008. [PubMed:18412191 ]
LOTUS database [Link]

Showing NP-Card for 2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid (NP0215595)

MOL for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

3D MOL for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

3D SDF for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

3D-SDF for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

PDB for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

3D PDB for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

SMILES for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

INCHI for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

Structure for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)

3D Structure for NP0215595 (2-[(2s,3s,6r)-3-[(2-amino-1,3-dihydroxypropylidene)amino]-6-[2-hydroxy-5-(hydroxymethyl)-4-iminopyrimidin-1-yl]-3,6-dihydro-2h-pyran-2-yl]-5-carbamimidamido-2,4-dihydroxypentanoic acid)