Chemical Components in the PDB

pdbe.org/chem
spacer

2H5 : Summary

Code

2H5

One-letter code

X

Molecule name

3-deoxy-3-fluoro-beta-D-galactopyranose

Systematic names

ProgramVersionName
ACDLabs 12.01 3-deoxy-3-fluoro-beta-D-galactopyranose
OpenEye OEToolkits 1.7.6 (2R,3S,4S,5S,6R)-4-fluoranyl-6-(hydroxymethyl)oxane-2,3,5-triol

Formula

C6 H11 F O5

Formal charge

0

Molecular weight

182.147 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC1C(O)C(OC(O)C1O)CO
SMILES CACTVS 3.385 OC[CH]1O[CH](O)[CH](O)[CH](F)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C(C1C(C(C(C(O1)O)O)F)O)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](F)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O)O)F)O)O

IUPAC InChI

InChI=1S/C6H11FO5/c7-3-4(9)2(1-8)12-6(11)5(3)10/h2-6,8-11H,1H2/t2-,3+,4+,5-,6-/m1/s1

IUPAC InChI key

BUMRBAMACDBPKO-FPRJBGLDSA-N
2H5

wwPDB Information

Atom count

23 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-10-18

Last modified at

2014-01-31

Status

Released

Obsoleted

Not Assigned



2H5 : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -0.476 -1.438 -0.192
2 C2 C C2 S N N 0 -1.501 -0.35 0.137
3 C3 C C3 S N N 0 -1.105 0.947 -0.574
4 C4 C C4 S N N 0 0.314 1.337 -0.147
5 C5 C C5 R N N 0 1.269 0.185 -0.467
6 C6 C C6 N N N 0 2.678 0.542 0.011
7 F3 F F3 N N N 0 -1.996 1.966 -0.22
8 H1 H H1 N N N 0 -1.523 -0.183 1.214
9 H10 H H10 N N N 0 -0.252 2.318 1.532
10 H11 H H11 N N N 0 4.506 -0.32 -0.12
11 H2 H H2 N N N 0 2.981 1.492 -0.429
12 H3 H H3 N N N 0 2.682 0.628 1.098
13 H4 H H4 N N N 0 -1.134 0.796 -1.653
14 H5 H H5 N N N 0 0.625 2.23 -0.69
15 H6 H H6 N N N 0 1.283 0.012 -1.543
16 H7 H H7 N N N 0 -0.485 -1.634 -1.264
17 H8 H H8 N N N 0 -0.2 -3.369 0.352
18 H9 H H9 N N N 0 -3.109 -1.581 0.1
19 O1 O O1 N N N 0 -0.809 -2.636 0.514
20 O2 O O2 N N N 0 -2.795 -0.762 -0.308
21 O4 O O4 N N N 0 0.335 1.6 1.257
22 O5 O O5 N N N 0 0.826 -0.999 0.201
23 O6 O O6 N N N 0 3.591 -0.481 -0.39



2H5 : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C sing 1.43 N N
2 C6 C5 C C sing 1.53 N N
3 C5 C4 C C sing 1.53 N N
4 C5 O5 C O sing 1.43 N N
5 C4 C3 C C sing 1.53 N N
6 C4 O4 C O sing 1.43 N N
7 O5 C1 O C sing 1.43 N N
8 C3 C2 C C sing 1.53 N N
9 C3 F3 C F sing 1.4 N N
10 C1 C2 C C sing 1.53 N N
11 C1 O1 C O sing 1.43 N N
12 C2 O2 C O sing 1.43 N N
13 C2 H1 C H sing 1.09 N N
14 C6 H2 C H sing 1.09 N N
15 C6 H3 C H sing 1.09 N N
16 C3 H4 C H sing 1.09 N N
17 C4 H5 C H sing 1.09 N N
18 C5 H6 C H sing 1.09 N N
19 C1 H7 C H sing 1.09 N N
20 O1 H8 O H sing 0.97 N N
21 O2 H9 O H sing 0.97 N N
22 O4 H10 O H sing 0.97 N N
23 O6 H11 O H sing 0.97 N N



2H5 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
2H5 4mom Open in New Window Bound ligand 4 1
2H5 4mop Open in New Window Bound ligand 4 1
2H5 4mor Open in New Window Bound ligand 4 1