NP-MRD: Showing NP-Card for N-Succinyl-L,L-2,6-diaminopimelate (NP0334810)

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Record Information

Version

2.0

Created at

2024-09-10 20:03:43 UTC

Updated at

2024-09-10 20:03:43 UTC

NP-MRD ID

NP0334810

Secondary Accession Numbers

None

Natural Product Identification

Common Name

N-Succinyl-L,L-2,6-diaminopimelate

Description

N-Succinyl-L,L-2,6-diaminopimelate, also known as N-succinyl-L-2,6-diaminoheptanedioate or L,L-sdap, belongs to the class of organic compounds known as n-acyl-l-alpha-amino acids. These are n-acylated alpha amino acids which have the L-configuration of the alpha-carbon atom. N-Succinyl-L,L-2,6-diaminopimelate is a very strong basic compound (based on its pKa). N-Succinyl-L,L-2,6-diaminopimelate exists in all living organisms, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241203542D          

 20 19  0  0  1  0            999 V2000
   11.0481   -6.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2231   -6.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4606   -6.1717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4606   -4.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0481   -5.4572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -7.6007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2856   -6.1717    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2856   -4.7428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2231   -5.4572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.2231   -8.3151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6981   -6.8862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9855   -7.6007    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6981   -5.4572    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6981   -4.0283    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -4.7428    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -6.1717    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8106   -9.0296    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0481   -8.3151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2856   -7.6007    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5231   -6.8862    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  6  1  0  0  0  0
  7  3  1  6  0  0  0
  4  8  1  0  0  0  0
  4  5  1  0  0  0  0
  5  9  1  0  0  0  0
  6 12  1  0  0  0  0
  6 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 13  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  2  0  0  0  0
  9 15  1  0  0  0  0
  9 16  2  0  0  0  0
 10 17  1  0  0  0  0
 10 18  2  0  0  0  0
 11 19  1  0  0  0  0
 11 20  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0334810

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCC[C@H](NC(=O)CCC(O)=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/t6?,7-/m0/s1

> <INCHI_KEY>
GLXUWZBUPATPBR-MLWJPKLSSA-N

> <FORMULA>
C11H18N2O7

> <MOLECULAR_WEIGHT>
290.2698

> <EXACT_MASS>
290.11140094

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
27.089310391348025

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

> <ALOGPS_LOGP>
-3.08

> <JCHEM_LOGP>
-3.767654759825556

> <ALOGPS_LOGS>
-1.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.5652463088565987

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.887292954138168

> <JCHEM_PKA_STRONGEST_BASIC>
9.526516455366492

> <JCHEM_POLAR_SURFACE_AREA>
167.01999999999998

> <JCHEM_REFRACTIVITY>
63.97650000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.80e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      20.623 -12.854   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      19.083 -12.854   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.393 -11.521   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.393  -8.853   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.623 -10.187   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.313 -14.188   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.933 -11.521   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.933  -8.853   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.083 -10.187   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      19.083 -15.522   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.703 -12.854   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      16.773 -14.188   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      23.703 -10.187   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      23.703  -7.519   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      18.313  -8.853   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      18.313 -11.521   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      18.313 -16.855   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      20.623 -15.522   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      22.933 -14.188   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      25.243 -12.854   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    7                                                       
CONECT    4    8    5                                                       
CONECT    5    4    9                                                       
CONECT    6    2   12   10                                                  
CONECT    7    3   11   13                                                  
CONECT    8    4   13   14                                                  
CONECT    9    5   15   16                                                  
CONECT   10    6   17   18                                                  
CONECT   11    7   19   20                                                  
CONECT   12    6                                                            
CONECT   13    7    8                                                       
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18   10                                                            
CONECT   19   11                                                            
CONECT   20   11                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

View in JSmol

Synonyms

Value	Source
N-Succinyl-L,L-2,6-diaminopimelic acid	Generator
L,L-Sdap	HMDB
N-Succinyl-L-2,6-diaminoheptanedioate	HMDB
N-Succinyl-L-2,6-diaminoheptanedioic acid	HMDB
N-Succinyl-LL-2,6-diaminoheptanedioate	HMDB
N-Succinyl-LL-2,6-diaminoheptanedioic acid	HMDB
N-Succinyl-LL-2,6-diaminopimelate	HMDB

Chemical Formula

C₁₁H₁₈N₂O₇

Average Mass

290.2698 Da

Monoisotopic Mass

290.11140 Da

IUPAC Name

(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

Traditional Name

(6S)-2-amino-6-(3-carboxypropanamido)heptanedioic acid

CAS Registry Number

Not Available

SMILES

NC(CCC[C@H](NC(=O)CCC(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/t6?,7-/m0/s1

InChI Key

GLXUWZBUPATPBR-MLWJPKLSSA-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 n-acyl-l-alpha-amino acids. These are n-acylated alpha amino acids which have the L-configuration of the alpha-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

N-acyl-L-alpha-amino acids

Alternative Parents

Substituents

N-acyl-l-alpha-amino acid
Alpha-amino acid
Tricarboxylic acid or derivatives
Amino fatty acid
Fatty amide
N-acyl-amine
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Amino acid
Carboxylic acid
Primary amine
Organooxygen compound
Organonitrogen compound
Organic oxide
Primary aliphatic amine
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Amine
Hydrocarbon derivative
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	-3.1	ALOGPS
logP	-3.8	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.89	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	167.02 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	63.98 m³·mol⁻¹	ChemAxon
Polarizability	27.09 Å³	ChemAxon
Number of Rings	0	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

HMDB ID

HMDB0012267

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB028905

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04421

BioCyc ID

N-SUCCINYLLL-2-6-DIAMINOPIMELATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25202447

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for N-Succinyl-L,L-2,6-diaminopimelate (NP0334810)

MOL for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

3D MOL for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

3D SDF for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

3D-SDF for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

PDB for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

3D PDB for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

SMILES for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

INCHI for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

Structure for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)

3D Structure for NP0334810 (N-Succinyl-L,L-2,6-diaminopimelate)