NP-MRD: Showing NP-Card for Dynorphin B (10-13) (NP0339125)

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Record Information

Version

2.0

Created at

2024-09-11 19:48:16 UTC

Updated at

2024-09-11 19:48:16 UTC

NP-MRD ID

NP0339125

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dynorphin B (10-13)

Description

Dynorphin B (10-13), also known as lys-val-val-THR, belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. Dynorphin B (10-13) is a very strong basic compound (based on its pKa). The peptide was called dynorphin (from the Greek dynamis=power) to describe its potency. The first clues to the functionality of dynorphins came from Goldstein et al. In their work with opioid peptides. Dynorphin B is a form of dynorphin.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303102016472D          

 31 30  0  0  1  0            999 V2000
   13.9847  -25.3282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2222  -24.6138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9222  -23.1848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6847  -23.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2721  -26.0427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -20.3269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847  -19.6124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847  -21.0413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -18.8979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -24.6138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5097  -23.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6847  -26.7572    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.3972  -21.7558    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.9847  -23.8993    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.9222  -24.6138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.5097  -26.7572    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.9847  -22.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1597  -23.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5097  -25.3282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9222  -27.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847  -18.1835    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.2222  -21.7558    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -23.1848    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.7472  -24.6138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9222  -26.0427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.2721  -27.4716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1597  -22.4703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7472  -23.1848    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6847  -25.3282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5097  -28.1861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7472  -27.4716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 11  1  0  0  0  0
 12  5  1  1  0  0  0
  6  8  1  0  0  0  0
  6  7  1  0  0  0  0
  7  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 21  1  0  0  0  0
 14 10  1  1  0  0  0
 15 11  1  1  0  0  0
 12 16  1  0  0  0  0
 12 26  1  0  0  0  0
 13 17  1  0  0  0  0
 13 22  1  1  0  0  0
 14 23  1  0  0  0  0
 14 18  1  0  0  0  0
 15 24  1  0  0  0  0
 15 19  1  0  0  0  0
 16 25  1  6  0  0  0
 16 20  1  0  0  0  0
 17 23  1  0  0  0  0
 17 27  2  0  0  0  0
 18 28  2  0  0  0  0
 18 24  1  0  0  0  0
 19 29  2  0  0  0  0
 19 25  1  0  0  0  0
 20 30  1  0  0  0  0
 20 31  2  0  0  0  0
M  END


  Mrv1652303102016472D          

 31 30  0  0  1  0            999 V2000
   13.9847  -25.3282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.2222  -24.6138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9222  -23.1848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6847  -23.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2721  -26.0427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -20.3269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847  -19.6124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847  -21.0413    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -18.8979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -24.6138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5097  -23.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6847  -26.7572    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.3972  -21.7558    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   13.9847  -23.8993    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.9222  -24.6138    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.5097  -26.7572    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.9847  -22.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1597  -23.8993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5097  -25.3282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9222  -27.4716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9847  -18.1835    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.2222  -21.7558    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.3972  -23.1848    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.7472  -24.6138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.9222  -26.0427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.2721  -27.4716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.1597  -22.4703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7472  -23.1848    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6847  -25.3282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5097  -28.1861    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7472  -27.4716    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 11  1  0  0  0  0
 12  5  1  1  0  0  0
  6  8  1  0  0  0  0
  6  7  1  0  0  0  0
  7  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 21  1  0  0  0  0
 14 10  1  1  0  0  0
 15 11  1  1  0  0  0
 12 16  1  0  0  0  0
 12 26  1  0  0  0  0
 13 17  1  0  0  0  0
 13 22  1  1  0  0  0
 14 23  1  0  0  0  0
 14 18  1  0  0  0  0
 15 24  1  0  0  0  0
 15 19  1  0  0  0  0
 16 25  1  6  0  0  0
 16 20  1  0  0  0  0
 17 23  1  0  0  0  0
 17 27  2  0  0  0  0
 18 28  2  0  0  0  0
 18 24  1  0  0  0  0
 19 29  2  0  0  0  0
 19 25  1  0  0  0  0
 20 30  1  0  0  0  0
 20 31  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0339125

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H](NC(=O)[C@H](N)CCCCN)C(=O)N[C@H](C(C)C)C(=O)N[C@@H]([C@H](C)O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H39N5O6/c1-10(2)14(23-17(27)13(22)8-6-7-9-21)18(28)24-15(11(3)4)19(29)25-16(12(5)26)20(30)31/h10-16,26H,6-9,21-22H2,1-5H3,(H,23,27)(H,24,28)(H,25,29)(H,30,31)/t12-,13+,14-,15+,16-/m0/s1

> <INCHI_KEY>
VSLCIGXQLCYQTD-NPJQDHAYSA-N

> <FORMULA>
C20H39N5O6

> <MOLECULAR_WEIGHT>
445.5536

> <EXACT_MASS>
445.290034005

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
47.55766278408917

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S)-2-[(2R)-2-[(2S)-2-[(2R)-2,6-diaminohexanamido]-3-methylbutanamido]-3-methylbutanamido]-3-hydroxybutanoic acid

> <ALOGPS_LOGP>
-1.55

> <JCHEM_LOGP>
-3.5155954517408974

> <ALOGPS_LOGS>
-2.94

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.191194527853293

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3005841825961286

> <JCHEM_PKA_STRONGEST_BASIC>
10.202688606547488

> <JCHEM_POLAR_SURFACE_AREA>
196.86999999999998

> <JCHEM_REFRACTIVITY>
113.65539999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
14

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.13e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-2-[(2R)-2-[(2S)-2-[(2R)-2,6-diaminohexanamido]-3-methylbutanamido]-3-methylbutanamido]-3-hydroxybutanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      26.105 -47.279   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      28.415 -45.946   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.255 -43.278   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      19.945 -44.612   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      19.175 -48.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.875 -37.944   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      26.105 -36.610   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      26.105 -39.277   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      26.875 -35.276   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.875 -45.946   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      21.485 -44.612   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      19.945 -49.947   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      26.875 -40.611   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      26.105 -44.612   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.255 -45.946   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      21.485 -49.947   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.105 -41.945   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      24.565 -44.612   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      21.485 -47.279   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      22.255 -51.280   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      26.105 -33.943   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0      28.415 -40.611   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0      26.875 -43.278   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0      23.795 -45.946   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0      22.255 -48.613   0.000  0.00  0.00           N+0
HETATM   26  O   UNK     0      19.175 -51.280   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      24.565 -41.945   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      23.795 -43.278   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      19.945 -47.279   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      21.485 -52.614   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      23.795 -51.280   0.000  0.00  0.00           O+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6    8    7                                                       
CONECT    7    6    9                                                       
CONECT    8    6   13                                                       
CONECT    9    7   21                                                       
CONECT   10    1    2   14                                                  
CONECT   11    3    4   15                                                  
CONECT   12    5   16   26                                                  
CONECT   13    8   17   22                                                  
CONECT   14   10   23   18                                                  
CONECT   15   11   24   19                                                  
CONECT   16   12   25   20                                                  
CONECT   17   13   23   27                                                  
CONECT   18   14   28   24                                                  
CONECT   19   15   29   25                                                  
CONECT   20   16   30   31                                                  
CONECT   21    9                                                            
CONECT   22   13                                                            
CONECT   23   14   17                                                       
CONECT   24   15   18                                                       
CONECT   25   16   19                                                       
CONECT   26   12                                                            
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29   19                                                            
CONECT   30   20                                                            
CONECT   31   20                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   60    0
END

View in JSmol

Synonyms

Value	Source
Lys-val-val-THR	HMDB
(2S,3S)-2-{[(2R)-2-{[(2S)-2-{[(2R)-2,6-diamino-1-hydroxyhexylidene]amino}-1-hydroxy-3-methylbutylidene]amino}-1-hydroxy-3-methylbutylidene]amino}-3-hydroxybutanoate	Generator

Chemical Formula

C₂₀H₃₉N₅O₆

Average Mass

445.5536 Da

Monoisotopic Mass

445.29003 Da

IUPAC Name

(2S,3S)-2-[(2R)-2-[(2S)-2-[(2R)-2,6-diaminohexanamido]-3-methylbutanamido]-3-methylbutanamido]-3-hydroxybutanoic acid

Traditional Name

(2S,3S)-2-[(2R)-2-[(2S)-2-[(2R)-2,6-diaminohexanamido]-3-methylbutanamido]-3-methylbutanamido]-3-hydroxybutanoic acid

CAS Registry Number

Not Available

SMILES

CC(C)[C@H](NC(=O)[C@H](N)CCCCN)C(=O)N[C@H](C(C)C)C(=O)N[C@@H]([C@H](C)O)C(O)=O

InChI Identifier

InChI=1S/C20H39N5O6/c1-10(2)14(23-17(27)13(22)8-6-7-9-21)18(28)24-15(11(3)4)19(29)25-16(12(5)26)20(30)31/h10-16,26H,6-9,21-22H2,1-5H3,(H,23,27)(H,24,28)(H,25,29)(H,30,31)/t12-,13+,14-,15+,16-/m0/s1

InChI Key

VSLCIGXQLCYQTD-NPJQDHAYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Valine or derivatives
N-acyl-l-alpha-amino acid
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
N-substituted-alpha-amino acid
Alpha-amino acid or derivatives
Beta-hydroxy acid
Branched fatty acid
Hydroxy fatty acid
Short-chain hydroxy acid
Fatty amide
Hydroxy acid
N-acyl-amine
Fatty acyl
Fatty acid
Secondary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Amino acid
Carboxamide group
Monocarboxylic acid or derivatives
Carboxylic acid
Organopnictogen compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Primary aliphatic amine
Organic oxide
Organic nitrogen compound
Amine
Organonitrogen compound
Organooxygen compound
Primary amine
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	-1.6	ALOGPS
logP	-3.5	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	3.3	ChemAxon
pKa (Strongest Basic)	10.2	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	196.87 Å²	ChemAxon
Rotatable Bond Count	14	ChemAxon
Refractivity	113.66 m³·mol⁻¹	ChemAxon
Polarizability	47.56 Å³	ChemAxon
Number of Rings	0	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

HMDB0012936

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029216

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53481556

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Dynorphin B (10-13) (NP0339125)

MOL for NP0339125 (Dynorphin B (10-13))

3D MOL for NP0339125 (Dynorphin B (10-13))

3D SDF for NP0339125 (Dynorphin B (10-13))

3D-SDF for NP0339125 (Dynorphin B (10-13))

PDB for NP0339125 (Dynorphin B (10-13))

3D PDB for NP0339125 (Dynorphin B (10-13))

SMILES for NP0339125 (Dynorphin B (10-13))

INCHI for NP0339125 (Dynorphin B (10-13))

Structure for NP0339125 (Dynorphin B (10-13))

3D Structure for NP0339125 (Dynorphin B (10-13))