NP-MRD: Showing NP-Card for Dynorphin A 1-8 (NP0339122)

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Record Information

Version

2.0

Created at

2024-09-11 19:47:32 UTC

Updated at

2024-09-11 19:47:32 UTC

NP-MRD ID

NP0339122

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dynorphin A 1-8

Description

Dynorphin A 1-8 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. Dynorphin A 1-8 is a very strong basic compound (based on its pKa). Although KOR is the primary receptor for all dynorphins, the peptides do have some affinity for the μ-opioid receptor (MOR), d-opioid receptor (DOR), N-methyl-D-aspartic acid (NMDA)-type glutamate receptor. Dense-core vesicle storage is characteristic of opioid peptides storage. 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.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303102016472D          

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M  END


  Mrv1652303102016472D          

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 60 61  1  0  0  0  0
 61 62  1  0  0  0  0
 61 67  2  0  0  0  0
 62 63  2  0  0  0  0
 63 64  1  0  0  0  0
 64 65  1  0  0  0  0
 64 66  2  0  0  0  0
 66 67  1  0  0  0  0
 68 69  1  0  0  0  0
 68 70  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0339122

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)[C@H](NC(=O)[C@@H](CCCNC(N)=N)NC(=O)[C@@H](CCCNC(N)=N)NC(=O)C(CC(C)C)NC(=O)[C@@H](CC1=CC=CC=C1)NC(=O)CNC(=O)CNC(=O)[C@@H](N)CC1=CC=C(O)C=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C46H72N14O10/c1-5-27(4)38(44(69)70)60-41(66)33(14-10-20-53-46(50)51)57-40(65)32(13-9-19-52-45(48)49)58-42(67)34(21-26(2)3)59-43(68)35(23-28-11-7-6-8-12-28)56-37(63)25-54-36(62)24-55-39(64)31(47)22-29-15-17-30(61)18-16-29/h6-8,11-12,15-18,26-27,31-35,38,61H,5,9-10,13-14,19-25,47H2,1-4H3,(H,54,62)(H,55,64)(H,56,63)(H,57,65)(H,58,67)(H,59,68)(H,60,66)(H,69,70)(H4,48,49,52)(H4,50,51,53)/t27-,31-,32+,33+,34?,35+,38-/m0/s1

> <INCHI_KEY>
WRPLGMBDXVBPEG-PUGOIMMUSA-N

> <FORMULA>
C46H72N14O10

> <MOLECULAR_WEIGHT>
981.1517

> <EXACT_MASS>
980.555584594

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
142

> <JCHEM_AVERAGE_POLARIZABILITY>
103.70653007976495

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
16

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S)-2-[(2R)-2-[(2R)-2-{2-[(2R)-2-(2-{2-[(2S)-2-amino-3-(4-hydroxyphenyl)propanamido]acetamido}acetamido)-3-phenylpropanamido]-4-methylpentanamido}-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-3-methylpentanoic acid

> <ALOGPS_LOGP>
-1.61

> <JCHEM_LOGP>
-5.468164680096957

> <ALOGPS_LOGS>
-4.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
9.507780639073777

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.559637176412647

> <JCHEM_PKA_STRONGEST_BASIC>
12.177386934436287

> <JCHEM_POLAR_SURFACE_AREA>
411.04999999999995

> <JCHEM_REFRACTIVITY>
277.9320000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
31

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.23e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-2-[(2R)-2-[(2R)-2-{2-[(2R)-2-(2-{2-[(2S)-2-amino-3-(4-hydroxyphenyl)propanamido]acetamido}acetamido)-3-phenylpropanamido]-4-methylpentanamido}-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       9.860 -15.245   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.196 -16.010   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      11.201 -17.550   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.869 -18.324   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.537 -18.316   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      13.868 -17.542   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      15.204 -18.308   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      15.209 -19.848   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      16.535 -17.534   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.531 -15.994   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.195 -15.228   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      15.190 -13.688   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      13.854 -12.922   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      13.849 -11.382   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      12.513 -10.616   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      15.180 -10.608   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      17.871 -18.299   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0      19.203 -17.525   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      19.198 -15.985   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      20.539 -18.291   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      21.870 -17.517   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      21.865 -15.977   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      23.197 -15.203   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      24.404 -15.895   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      25.607 -15.195   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      26.815 -15.888   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0      25.603 -13.803   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0      20.565 -19.873   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      21.902 -20.639   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      23.233 -19.865   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      21.906 -22.179   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      20.575 -22.953   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      19.239 -22.187   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      19.234 -20.647   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      17.908 -22.961   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0      23.242 -22.945   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0      23.247 -24.485   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      21.916 -25.259   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      24.583 -25.250   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      24.588 -26.790   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      25.924 -27.556   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      27.255 -26.782   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      28.592 -27.548   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      28.596 -29.088   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      27.265 -29.862   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      25.929 -29.096   0.000  0.00  0.00           C+0
HETATM   47  N   UNK     0      25.915 -24.476   0.000  0.00  0.00           N+0
HETATM   48  C   UNK     0      25.910 -22.936   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      24.574 -22.170   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0      27.241 -22.162   0.000  0.00  0.00           C+0
HETATM   51  N   UNK     0      27.236 -20.622   0.000  0.00  0.00           N+0
HETATM   52  C   UNK     0      28.567 -19.848   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      28.563 -18.308   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      29.903 -20.614   0.000  0.00  0.00           C+0
HETATM   55  N   UNK     0      31.235 -19.840   0.000  0.00  0.00           N+0
HETATM   56  C   UNK     0      32.571 -20.606   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0      32.576 -22.146   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0      33.902 -19.831   0.000  0.00  0.00           C+0
HETATM   59  N   UNK     0      33.897 -18.291   0.000  0.00  0.00           N+0
HETATM   60  C   UNK     0      35.238 -20.597   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      36.569 -19.823   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      37.905 -20.589   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      39.237 -19.815   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      39.232 -18.275   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0      40.563 -17.501   0.000  0.00  0.00           O+0
HETATM   66  C   UNK     0      37.896 -17.509   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      36.565 -18.283   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      12.542 -19.856   0.000  0.00  0.00           C+0
HETATM   69  O   UNK     0      11.210 -20.630   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      13.878 -20.622   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   68                                                  
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   28                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   20   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   31   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   47                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42   46                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   41   45                                                       
CONECT   47   39   48                                                       
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53   54                                                  
CONECT   53   52                                                            
CONECT   54   52   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57   58                                                  
CONECT   57   56                                                            
CONECT   58   56   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62   67                                                  
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65   66                                                  
CONECT   65   64                                                            
CONECT   66   64   67                                                       
CONECT   67   61   66                                                       
CONECT   68    5   69   70                                                  
CONECT   69   68                                                            
CONECT   70   68                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  142    0
END

View in JSmol

Synonyms

Value	Source
Dynorphin a (1-8)	HMDB
Dynorphin a fragment 1-8	HMDB
Tyr-gly-gly-phe-leu-arg-arg-ile	HMDB
(2S,3S)-2-{[(2R)-2-{[(2R)-2-[(2-{[(2R)-2-({2-[(2-{[(2S)-2-amino-1-hydroxy-3-(4-hydroxyphenyl)propylidene]amino}-1-hydroxyethylidene)amino]-1-hydroxyethylidene}amino)-1-hydroxy-3-phenylpropylidene]amino}-1-hydroxy-4-methylpentylidene)amino]-5-carbamimidamido-1-hydroxypentylidene]amino}-5-carbamimidamido-1-hydroxypentylidene]amino}-3-methylpentanoate	Generator
Dynorphin (1-8)	MeSH
Tyrosyl-glycyl-glycyl-phenylalanyl--leucyl-arginyl-arginyl-isoleucine	MeSH
PH-8P	MeSH

Chemical Formula

C₄₆H₇₂N₁₄O₁₀

Average Mass

981.1517 Da

Monoisotopic Mass

980.55558 Da

IUPAC Name

(2S,3S)-2-[(2R)-2-[(2R)-2-{2-[(2R)-2-(2-{2-[(2S)-2-amino-3-(4-hydroxyphenyl)propanamido]acetamido}acetamido)-3-phenylpropanamido]-4-methylpentanamido}-5-carbamimidamidopentanamido]-5-carbamimidamidopentanamido]-3-methylpentanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

CC[C@H](C)[C@H](NC(=O)[C@@H](CCCNC(N)=N)NC(=O)[C@@H](CCCNC(N)=N)NC(=O)C(CC(C)C)NC(=O)[C@@H](CC1=CC=CC=C1)NC(=O)CNC(=O)CNC(=O)[C@@H](N)CC1=CC=C(O)C=C1)C(O)=O

InChI Identifier

InChI=1S/C46H72N14O10/c1-5-27(4)38(44(69)70)60-41(66)33(14-10-20-53-46(50)51)57-40(65)32(13-9-19-52-45(48)49)58-42(67)34(21-26(2)3)59-43(68)35(23-28-11-7-6-8-12-28)56-37(63)25-54-36(62)24-55-39(64)31(47)22-29-15-17-30(61)18-16-29/h6-8,11-12,15-18,26-27,31-35,38,61H,5,9-10,13-14,19-25,47H2,1-4H3,(H,54,62)(H,55,64)(H,56,63)(H,57,65)(H,58,67)(H,59,68)(H,60,66)(H,69,70)(H4,48,49,52)(H4,50,51,53)/t27-,31-,32+,33+,34?,35+,38-/m0/s1

InChI Key

WRPLGMBDXVBPEG-PUGOIMMUSA-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	-1.6	ALOGPS
logP	-5.5	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	3.56	ChemAxon
pKa (Strongest Basic)	12.18	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	16	ChemAxon
Polar Surface Area	411.05 Å²	ChemAxon
Rotatable Bond Count	31	ChemAxon
Refractivity	277.93 m³·mol⁻¹	ChemAxon
Polarizability	103.71 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

HMDB0012933

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029213

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dynorphin A

METLIN ID

Not Available

PubChem Compound

53481552

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Dynorphin A 1-8 (NP0339122)

MOL for NP0339122 (Dynorphin A 1-8)

3D MOL for NP0339122 (Dynorphin A 1-8)

3D SDF for NP0339122 (Dynorphin A 1-8)

3D-SDF for NP0339122 (Dynorphin A 1-8)

PDB for NP0339122 (Dynorphin A 1-8)

3D PDB for NP0339122 (Dynorphin A 1-8)

SMILES for NP0339122 (Dynorphin A 1-8)

INCHI for NP0339122 (Dynorphin A 1-8)

Structure for NP0339122 (Dynorphin A 1-8)

3D Structure for NP0339122 (Dynorphin A 1-8)