Chemical Components in the PDB

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LDU : Summary

Code

LDU

One-letter code

X

Molecule name

DIDEOXY-IMINO-LYXITOL

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 (2R,3S,4R)-2-(hydroxymethyl)pyrrolidine-3,4-diol

Formula

C5 H11 N O3

Formal charge

0

Molecular weight

133.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH]1NC[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C1C(C(C(N1)CO)O)O
Canonical SMILES CACTVS 3.385 OC[C@H]1NC[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1[C@H]([C@H]([C@H](N1)CO)O)O

IUPAC InChI

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

OQEBIHBLFRADNM-WDCZJNDASA-N
LDU

wwPDB Information

Atom count

20 (9 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-03-17

Last modified at

2015-03-20

Status

Released

Obsoleted

Not Assigned



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 Bound ligand 1 1