NP-MRD: Showing NP-Card for Dynorphin A (6-8) (NP0339121)

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Record Information

Version

2.0

Created at

2024-09-11 19:47:15 UTC

Updated at

2024-09-11 19:47:15 UTC

NP-MRD ID

NP0339121

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dynorphin A (6-8)

Description

Dynorphin A (6-8) 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. The peptide was called dynorphin (from the Greek dynamis=power) to describe its potency. Dynorphin A (6-8) is a very strong basic compound (based on its pKa). These data reveal a mechanism for endogenous dynorphin to promote pain through its agonist action at bradykinin receptors and suggest new avenues for therapeutic intervention. Dynorphin A is a form of dynorphin.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303102016472D          

 31 30  0  0  1  0            999 V2000
   14.2682  -10.7796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -11.4665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5057  -11.4665    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.9182  -10.7521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9182  -12.1810    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5057  -12.8955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -12.8955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3228  -12.1723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -13.6100    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6807  -14.3245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -15.0390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -15.7534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -16.4679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -17.1824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -17.8969    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.5057  -17.1824    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.4432  -13.6100    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.0307  -12.8955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4432  -12.1810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056  -12.8955    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.7931  -13.6100    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.7931  -12.1810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056  -11.4665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7931  -10.7521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056  -10.0376    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.7931   -9.3231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056   -8.6087    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9681   -9.3231    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7432  -12.1810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1557  -12.8955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1557  -11.4665    0.0000 O   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  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 29  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 17  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
M  END


  Mrv1652303102016472D          

 31 30  0  0  1  0            999 V2000
   14.2682  -10.7796    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -11.4665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5057  -11.4665    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.9182  -10.7521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9182  -12.1810    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5057  -12.8955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -12.8955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3228  -12.1723    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -13.6100    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6807  -14.3245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -15.0390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -15.7534    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -16.4679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.6807  -17.1824    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2682  -17.8969    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.5057  -17.1824    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.4432  -13.6100    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.0307  -12.8955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4432  -12.1810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056  -12.8955    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.7931  -13.6100    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.7931  -12.1810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056  -11.4665    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7931  -10.7521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056  -10.0376    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.7931   -9.3231    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2056   -8.6087    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9681   -9.3231    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7432  -12.1810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1557  -12.8955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1557  -11.4665    0.0000 O   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  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 29  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 17  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  6  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 29 30  1  0  0  0  0
 29 31  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0339121

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C18H37N9O4/c1-3-10(2)13(16(30)31)27-15(29)12(7-5-9-25-18(22)23)26-14(28)11(19)6-4-8-24-17(20)21/h10-13H,3-9,19H2,1-2H3,(H,26,28)(H,27,29)(H,30,31)(H4,20,21,24)(H4,22,23,25)/t10-,11-,12+,13-/m1/s1

> <INCHI_KEY>
BHSYMWWMVRPCPA-FVCCEPFGSA-N

> <FORMULA>
C18H37N9O4

> <MOLECULAR_WEIGHT>
443.5443

> <EXACT_MASS>
443.296850717

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
48.143228908699236

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-2-[(2S)-2-[(2R)-2-amino-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-3-methylpentanoic acid

> <ALOGPS_LOGP>
-3.46

> <JCHEM_LOGP>
-4.146813157816249

> <ALOGPS_LOGS>
-3.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
12.787057104899208

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6247760025811826

> <JCHEM_PKA_STRONGEST_BASIC>
12.177864512970407

> <JCHEM_POLAR_SURFACE_AREA>
245.32

> <JCHEM_REFRACTIVITY>
135.5403

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.57e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-2-[(2S)-2-[(2R)-2-amino-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-3-methylpentanoic 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      26.634 -20.122   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      27.404 -21.404   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      28.944 -21.404   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      29.714 -20.071   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.714 -22.738   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      28.944 -24.072   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      27.404 -24.072   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      26.736 -22.722   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      26.634 -25.405   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      27.404 -26.739   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.634 -28.073   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      27.404 -29.406   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      26.634 -30.740   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      27.404 -32.074   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      26.634 -33.408   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      28.944 -32.074   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      25.094 -25.405   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      24.324 -24.072   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      25.094 -22.738   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      22.784 -24.072   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      22.014 -25.405   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      22.014 -22.738   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      22.784 -21.404   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      22.014 -20.071   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      22.784 -18.737   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      22.014 -17.403   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      22.784 -16.070   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0      20.474 -17.403   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      31.254 -22.738   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      32.024 -24.072   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      32.024 -21.404   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   29                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    9   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29    5   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   60    0
END

View in JSmol

Synonyms

Value	Source
(2R,3R)-2-{[(2S)-2-{[(2R)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}-5-carbamimidamido-1-hydroxypentylidene]amino}-3-methylpentanoate	Generator

Chemical Formula

C₁₈H₃₇N₉O₄

Average Mass

443.5443 Da

Monoisotopic Mass

443.29685 Da

IUPAC Name

(2R,3R)-2-[(2S)-2-[(2R)-2-amino-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-3-methylpentanoic acid

Traditional Name

(2R,3R)-2-[(2S)-2-[(2R)-2-amino-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-3-methylpentanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C18H37N9O4/c1-3-10(2)13(16(30)31)27-15(29)12(7-5-9-25-18(22)23)26-14(28)11(19)6-4-8-24-17(20)21/h10-13H,3-9,19H2,1-2H3,(H,26,28)(H,27,29)(H,30,31)(H4,20,21,24)(H4,22,23,25)/t10-,11-,12+,13-/m1/s1

InChI Key

BHSYMWWMVRPCPA-FVCCEPFGSA-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
Isoleucine or derivatives
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
Branched fatty acid
Methyl-branched fatty acid
Fatty amide
N-acyl-amine
Fatty acyl
Fatty acid
Amino acid or derivatives
Carboxamide group
Amino acid
Guanidine
Secondary carboxylic acid amide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Carboximidamide
Monocarboxylic acid or derivatives
Carboxylic acid
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Primary aliphatic amine
Organic nitrogen compound
Carbonyl group
Organic oxide
Organonitrogen compound
Organooxygen compound
Primary amine
Amine
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	-3.5	ALOGPS
logP	-4.1	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	3.62	ChemAxon
pKa (Strongest Basic)	12.18	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	245.32 Å²	ChemAxon
Rotatable Bond Count	15	ChemAxon
Refractivity	135.54 m³·mol⁻¹	ChemAxon
Polarizability	48.14 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

HMDB0012932

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029212

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

53481551

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Dynorphin A (6-8) (NP0339121)

MOL for NP0339121 (Dynorphin A (6-8))

3D MOL for NP0339121 (Dynorphin A (6-8))

3D SDF for NP0339121 (Dynorphin A (6-8))

3D-SDF for NP0339121 (Dynorphin A (6-8))

PDB for NP0339121 (Dynorphin A (6-8))

3D PDB for NP0339121 (Dynorphin A (6-8))

SMILES for NP0339121 (Dynorphin A (6-8))

INCHI for NP0339121 (Dynorphin A (6-8))

Structure for NP0339121 (Dynorphin A (6-8))

3D Structure for NP0339121 (Dynorphin A (6-8))