NP-MRD: Showing NP-Card for Nectrisine (NP0007418)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2020-12-09 04:18:08 UTC

Updated at

2021-07-15 16:57:32 UTC

NP-MRD ID

NP0007418

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nectrisine

Provided By

NPAtlas

Description

(2R,3R,4S)-2-(hydroxymethyl)-3,4-dihydro-2H-pyrrole-3,4-diol is also known as 3,4-dihydroxy-2-(hydroxymethyl)pyrrolidine or nectrisine. Nectrisine is found in Nectria, Nectria lucida F-4490 and Thelonectria lucida. Nectrisine was first documented in 1991 (PMID: 1799935). Based on a literature review very few articles have been published on (2R,3R,4S)-2-(hydroxymethyl)-3,4-dihydro-2H-pyrrole-3,4-diol.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118403D          

 18 18  0  0  0  0            999 V2000
    1.9215    1.1880   -0.3724 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9575   -0.1593   -0.0683 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6109   -0.7123    0.3085 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0362   -0.0889    1.4403 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9344    0.6660    1.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1643    0.6564   -0.2895 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5166    0.5448   -0.6110 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4076   -0.5520   -0.7934 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2558   -1.6672   -0.8495 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7046    1.6659    0.0135 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6476   -0.2837    0.7909 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3727   -0.7298   -0.9107 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7303   -1.7924    0.5156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5573    1.2683    1.8494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7422    1.5819   -0.7772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0181    0.6506    0.2564 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0932   -0.3630   -1.7715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4782   -1.8734    0.1076 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8  3  1  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  2 12  1  0  0  0  0
  3 13  1  1  0  0  0
  5 14  1  0  0  0  0
  6 15  1  6  0  0  0
  7 16  1  0  0  0  0
  8 17  1  6  0  0  0
  9 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0007418

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@@]1([H])N=C([H])[C@]([H])(O[H])[C@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO3/c7-2-3-5(9)4(8)1-6-3/h1,3-5,7-9H,2H2/t3-,4+,5-/m1/s1

> <INCHI_KEY>
QUPCOXZVKXONSC-MROZADKFSA-N

> <FORMULA>
C5H9NO3

> <MOLECULAR_WEIGHT>
131.131

> <EXACT_MASS>
131.058243154

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.348494516972753

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S)-2-(hydroxymethyl)-3,4-dihydro-2H-pyrrole-3,4-diol

> <ALOGPS_LOGP>
-1.81

> <JCHEM_LOGP>
-2.183110973333333

> <ALOGPS_LOGS>
-0.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.204765529987231

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.879368925365338

> <JCHEM_PKA_STRONGEST_BASIC>
4.126916718190888

> <JCHEM_POLAR_SURFACE_AREA>
73.05000000000001

> <JCHEM_REFRACTIVITY>
30.075599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.35e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S)-2-(hydroxymethyl)-3,4-dihydro-2H-pyrrole-3,4-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0       1.922   1.188  -0.372  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.958  -0.159  -0.068  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.611  -0.712   0.309  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.036  -0.089   1.440  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.934   0.666   1.161  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.164   0.656  -0.290  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.517   0.545  -0.611  0.00  0.00           O+0
HETATM    8  C   UNK     0      -0.408  -0.552  -0.793  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.256  -1.667  -0.850  0.00  0.00           O+0
HETATM   10  H   UNK     0       2.705   1.666   0.014  0.00  0.00           H+0
HETATM   11  H   UNK     0       2.648  -0.284   0.791  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.373  -0.730  -0.911  0.00  0.00           H+0
HETATM   13  H   UNK     0       0.730  -1.792   0.516  0.00  0.00           H+0
HETATM   14  H   UNK     0      -1.557   1.268   1.849  0.00  0.00           H+0
HETATM   15  H   UNK     0      -0.742   1.582  -0.777  0.00  0.00           H+0
HETATM   16  H   UNK     0      -3.018   0.651   0.256  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.093  -0.363  -1.772  0.00  0.00           H+0
HETATM   18  H   UNK     0      -1.478  -1.873   0.108  0.00  0.00           H+0
CONECT    1    2   10                                                       
CONECT    2    1    3   11   12                                             
CONECT    3    2    4    8   13                                             
CONECT    4    3    5                                                       
CONECT    5    4    6   14                                                  
CONECT    6    5    7    8   15                                             
CONECT    7    6   16                                                       
CONECT    8    6    9    3   17                                             
CONECT    9    8   18                                                       
CONECT   10    1                                                            
CONECT   11    2                                                            
CONECT   12    2                                                            
CONECT   13    3                                                            
CONECT   14    5                                                            
CONECT   15    6                                                            
CONECT   16    7                                                            
CONECT   17    8                                                            
CONECT   18    9                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
3,4-Dihydroxy-2-(hydroxymethyl)pyrrolidine	MeSH
3,4-Dihydroxy-5-hydroxymethyl-1-pyrroline	MeSH
Nectrisine	MeSH

Chemical Formula

C₅H₉NO₃

Average Mass

131.1310 Da

Monoisotopic Mass

131.05824 Da

IUPAC Name

(2R,3R,4S)-2-(hydroxymethyl)-3,4-dihydro-2H-pyrrole-3,4-diol

Traditional Name

(2R,3R,4S)-2-(hydroxymethyl)-3,4-dihydro-2H-pyrrole-3,4-diol

CAS Registry Number

Not Available

SMILES

OC[C@H]1N=C[C@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C5H9NO3/c7-2-3-5(9)4(8)1-6-3/h1,3-5,7-9H,2H2/t3-,4+,5-/m1/s1

InChI Key

QUPCOXZVKXONSC-MROZADKFSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Nectria	NPAtlas	1799935
Nectria lucida F-4490	Fungi	KNApSAcK
Thelonectria lucida	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	-0.25	ALOGPS
pKa (Strongest Acidic)	12.88	ChemAxon
pKa (Strongest Basic)	4.13	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.05 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	30.08 m³·mol⁻¹	ChemAxon
Polarizability	12.35 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA028476

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

108906

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

122106

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kayakiri H, Nakamura K, Takase S, Setoi H, Uchida I, Terano H, Hashimoto M, Tada T, Koda S: Structure and synthesis of nectrisine, a new immunomodulator isolated from a fungus. Chem Pharm Bull (Tokyo). 1991 Nov;39(11):2807-12. doi: 10.1248/cpb.39.2807. [PubMed:1799935 ]

Showing NP-Card for Nectrisine (NP0007418)

MOL for NP0007418 (Nectrisine)

3D MOL for NP0007418 (Nectrisine)

3D SDF for NP0007418 (Nectrisine)

3D-SDF for NP0007418 (Nectrisine)

PDB for NP0007418 (Nectrisine)

3D PDB for NP0007418 (Nectrisine)

SMILES for NP0007418 (Nectrisine)

INCHI for NP0007418 (Nectrisine)

Structure for NP0007418 (Nectrisine)

3D Structure for NP0007418 (Nectrisine)