3D structure for Glycyl-L-alpha-amino-epsilon-pimelyl-D-alanine (DB03927)

446307
  -OEChem-01032017253D

42 41  0     1  0  0  0  0  0999 V2000
   -4.6679   -2.5767   -1.1565 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2107   -1.7742    0.7371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0028   -1.8834    0.9783 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0410    1.3918   -1.2612 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8320    1.4794   -1.4905 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6470    0.4950   -0.5681 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6493    0.4374    0.3355 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1005    0.2655    0.0699 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9353    3.2042    0.5976 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7671   -0.4219   -0.2641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9640   -1.3365    0.0228 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5788   -1.0469    0.1075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3217   -0.7649   -0.3874 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7265   -0.0638   -0.1177 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0727   -0.6420    0.2820 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4218   -1.7671   -0.0931 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4821   -0.0313    0.3697 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.4889    1.4263   -0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8078    0.3617    1.8027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6301    2.5903    0.7956 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4317    0.6573   -0.5964 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7618   -0.1623   -1.3300 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8905    0.5167    0.2897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8094   -2.2914   -0.4967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   -1.5755    1.0949 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5603   -1.3562    1.1599 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7420   -1.9545   -0.4863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3361   -0.5342   -1.4592 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7740    0.2198   -1.1759 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5603    0.8474    0.4693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2824    0.5363    1.2779 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6290   -1.1102    0.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8779    1.1872   -0.2957 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6769    1.4391    1.9558 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1549   -0.1571    2.5128 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8450    0.1157    2.0538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8350    3.3108    0.5803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5320    2.2567    1.8334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3639   -3.2390   -0.9580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6672    2.5435    0.8567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0343    3.9964    1.2313 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4812    1.9062   -2.0893 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 16  1  0  0  0  0
  1 39  1  0  0  0  0
  2 15  2  0  0  0  0
  3 16  2  0  0  0  0
  4 18  2  0  0  0  0
  5 21  1  0  0  0  0
  5 42  1  0  0  0  0
  6 21  2  0  0  0  0
  7 13  1  0  0  0  0
  7 18  1  0  0  0  0
  7 31  1  0  0  0  0
  8 15  1  0  0  0  0
  8 17  1  0  0  0  0
  8 33  1  0  0  0  0
  9 20  1  0  0  0  0
  9 40  1  0  0  0  0
  9 41  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 22  1  0  0  0  0
 10 23  1  0  0  0  0
 11 13  1  0  0  0  0
 11 24  1  0  0  0  0
 11 25  1  0  0  0  0
 12 14  1  0  0  0  0
 12 26  1  0  0  0  0
 12 27  1  0  0  0  0
 13 16  1  0  0  0  0
 13 28  1  0  0  0  0
 14 15  1  0  0  0  0
 14 29  1  0  0  0  0
 14 30  1  0  0  0  0
 17 19  1  0  0  0  0
 17 21  1  0  0  0  0
 17 32  1  0  0  0  0
 18 20  1  0  0  0  0
 19 34  1  0  0  0  0
 19 35  1  0  0  0  0
 19 36  1  0  0  0  0
 20 37  1  0  0  0  0
 20 38  1  0  0  0  0
M  END
> <DATABASE_ID>
DB03927

> <DATABASE_NAME>
drugbank

> <ORIGINAL_SOURCE>
PUBCHEM

> <ORIGINAL_SOURCE_URL>
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/ZMQJQOKNTYQVHO-SFYZADRCSA-N/SDF?record_type=3d

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H21N3O6/c1-7(11(18)19)14-9(16)5-3-2-4-8(12(20)21)15-10(17)6-13/h7-8H,2-6,13H2,1H3,(H,14,16)(H,15,17)(H,18,19)(H,20,21)/t7-,8+/m1/s1

> <INCHI_KEY>
ZMQJQOKNTYQVHO-SFYZADRCSA-N

> <FORMULA>
C12H21N3O6

> <MOLECULAR_WEIGHT>
303.3116

> <EXACT_MASS>
303.143035419

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_NEUTRAL_MICROSPECIES_CHARGE>
-1.0662812644131143

> <JCHEM_AVERAGE_POLARIZABILITY>
30.140261487529592

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-(2-aminoacetamido)-6-{[(1R)-1-carboxyethyl]carbamoyl}hexanoic acid

> <JCHEM_LOGP>
-4.320308146512286

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NEUTRAL_CHARGE>
-1

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.9019137770209147

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.282683020616337

> <JCHEM_PKA_STRONGEST_BASIC>
8.139575861813762

> <JCHEM_POLAR_SURFACE_AREA>
158.82000000000002

> <JCHEM_REFRACTIVITY>
70.59060000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-({4-[(2E)-N-({2-amino-4-oxo-1H-pyrido[3,2-d]pyrimidin-6-yl}methyl)-3-{5-carbamoyl-3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]imidazol-4-yl}prop-2-enamido]phenyl}formamido)pentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

Similar Structures

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

3D structure for Glycyl-L-alpha-amino-epsilon-pimelyl-D-alanine (DB03927)

Structure for Glycyl-L-alpha-amino-epsilon-pimelyl-D-alanine (DB03927)