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LDU : Summary
Code ![](/pdbe/static/images/help.png)
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LDU
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One-letter code ![](/pdbe/static/images/help.png)
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X
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Molecule name ![](/pdbe/static/images/help.png)
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DIDEOXY-IMINO-LYXITOL
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Systematic names ![](/pdbe/static/images/help.png)
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Formula ![](/pdbe/static/images/help.png)
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C5 H11 N O3
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Formal charge ![](/pdbe/static/images/help.png)
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0
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Molecular weight ![](/pdbe/static/images/help.png)
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133.146 Da
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SMILES ![](/pdbe/static/images/help.png)
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Type | Program | Version | Descriptor |
SMILES
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CACTVS |
3.385 |
OC[CH]1NC[CH](O)[CH]1O |
SMILES
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OpenEye OEToolkits |
1.7.6 |
C1C(C(C(N1)CO)O)O |
Canonical SMILES
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CACTVS |
3.385 |
OC[C@H]1NC[C@@H](O)[C@H]1O |
Canonical SMILES
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OpenEye OEToolkits |
1.7.6 |
C1[C@H]([C@H]([C@H](N1)CO)O)O |
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IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4-,5+/m1/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | OQEBIHBLFRADNM-WDCZJNDASA-N |
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wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
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20 (9 without Hydrogen)
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Polymer type ![](/pdbe/static/images/help.png)
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Bound ligand
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Type description ![](/pdbe/static/images/help.png)
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non-polymer
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Type code ![](/pdbe/static/images/help.png)
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HETAIN
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Is modified ![](/pdbe/static/images/help.png)
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No
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Standard parent ![](/pdbe/static/images/help.png)
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Not Assigned
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Defined at ![](/pdbe/static/images/help.png)
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2015-03-17
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Last modified at ![](/pdbe/static/images/help.png)
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2015-03-20
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Status ![](/pdbe/static/images/help.png)
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Released
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Obsoleted ![](/pdbe/static/images/help.png)
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Not Assigned
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LDU : Atoms of Molecule
Total Number of Atoms: 20
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
O2 |
O |
O2 |
N |
N |
N |
0 |
0.442 |
1.77 |
-0.195 |
2 |
C4 |
C |
C4 |
S |
N |
N |
0 |
0.466 |
0.683 |
0.732 |
3 |
C3 |
C |
C3 |
R |
N |
N |
0 |
1.677 |
-0.231 |
0.455 |
4 |
O1 |
O |
O1 |
N |
N |
N |
0 |
2.433 |
0.268 |
-0.65 |
5 |
C2 |
C |
C2 |
N |
N |
N |
0 |
1.071 |
-1.609 |
0.112 |
6 |
N |
N |
N |
N |
N |
N |
0 |
-0.302 |
-1.304 |
-0.368 |
7 |
C5 |
C |
C5 |
R |
N |
N |
0 |
-0.771 |
-0.22 |
0.533 |
8 |
H2 |
H |
H2 |
N |
N |
N |
0 |
1.218 |
2.345 |
-0.146 |
9 |
C6 |
C |
C6 |
N |
N |
N |
0 |
-1.905 |
0.568 |
-0.126 |
10 |
O |
O |
O |
N |
N |
N |
0 |
-3.075 |
-0.249 |
-0.195 |
11 |
H4 |
H |
H4 |
N |
N |
N |
0 |
0.501 |
1.058 |
1.755 |
12 |
H3 |
H |
H3 |
N |
N |
N |
0 |
2.307 |
-0.304 |
1.342 |
13 |
H5 |
H |
H5 |
N |
N |
N |
0 |
-1.098 |
-0.633 |
1.487 |
14 |
H1 |
H |
H1 |
N |
N |
N |
0 |
3.208 |
-0.267 |
-0.87 |
15 |
H21C |
H |
H21C |
N |
N |
N |
0 |
1.649 |
-2.094 |
-0.674 |
16 |
H22C |
H |
H22C |
N |
N |
N |
0 |
1.032 |
-2.239 |
1.0 |
17 |
H |
H |
H |
N |
N |
N |
0 |
-0.289 |
-0.996 |
-1.329 |
18 |
H61C |
H |
H61C |
N |
N |
N |
0 |
-2.119 |
1.459 |
0.464 |
19 |
H62C |
H |
H62C |
N |
N |
N |
0 |
-1.607 |
0.862 |
-1.133 |
20 |
HA |
H |
HA |
N |
N |
N |
0 |
-3.836 |
0.187 |
-0.603 |
LDU : Chemical Bonds
Total Number of Bonds: 20
Record |
First Atom |
Second Atom |
First Element |
Second Element |
Bond Order Type |
Bond Length |
Bond Stereochemistry |
Is Aromatic |
1 |
O2 |
C4 |
O |
C |
sing |
1.43 |
N |
N |
2 |
C4 |
C3 |
C |
C |
sing |
1.54 |
N |
N |
3 |
C4 |
C5 |
C |
C |
sing |
1.54 |
N |
N |
4 |
C3 |
O1 |
C |
O |
sing |
1.43 |
N |
N |
5 |
C3 |
C2 |
C |
C |
sing |
1.54 |
N |
N |
6 |
C2 |
N |
C |
N |
sing |
1.49 |
N |
N |
7 |
N |
C5 |
N |
C |
sing |
1.49 |
N |
N |
8 |
C5 |
C6 |
C |
C |
sing |
1.53 |
N |
N |
9 |
C6 |
O |
C |
O |
sing |
1.43 |
N |
N |
10 |
O2 |
H2 |
O |
H |
sing |
0.97 |
N |
N |
11 |
C4 |
H4 |
C |
H |
sing |
1.09 |
N |
N |
12 |
C3 |
H3 |
C |
H |
sing |
1.09 |
N |
N |
13 |
C5 |
H5 |
C |
H |
sing |
1.09 |
N |
N |
14 |
O1 |
H1 |
O |
H |
sing |
0.97 |
N |
N |
15 |
C2 |
H21C |
C |
H |
sing |
1.09 |
N |
N |
16 |
C2 |
H22C |
C |
H |
sing |
1.09 |
N |
N |
17 |
N |
H |
N |
H |
sing |
1.01 |
N |
N |
18 |
C6 |
H61C |
C |
H |
sing |
1.09 |
N |
N |
19 |
C6 |
H62C |
C |
H |
sing |
1.09 |
N |
N |
20 |
O |
HA |
O |
H |
sing |
0.97 |
N |
N |
LDU : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
LDU |
4ufk ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724237634535) |
Bound ligand
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1 |
1 |
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