Chemical Components in the PDB

pdbe.org/chem
spacer

GL1 : Summary

Code

GL1

One-letter code

X

Molecule name

1-O-phosphono-alpha-D-galactopyranose

Synonyms

ALPHA-D-GALACTOSE-1-PHOSPHATE
1-O-phosphono-alpha-D-galactose
1-O-phosphono-D-galactose
1-O-phosphono-galactose

Systematic names

ProgramVersionName
ACDLabs 10.04 1-O-phosphono-alpha-D-galactopyranose
OpenEye OEToolkits 1.5.0 [(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] dihydrogen phosphate

Formula

C6 H13 O9 P

Formal charge

0

Molecular weight

260.136 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1O)CO)(O)O
SMILES CACTVS 3.341 OC[CH]1O[CH](O[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C(C1C(C(C(C(O1)OP(=O)(O)O)O)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@H]1O[C@H](O[P](O)(O)=O)[C@H](O)[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)O)O

IUPAC InChI

InChI=1S/C6H13O9P/c7-1-2-3(8)4(9)5(10)6(14-2)15-16(11,12)13/h2-10H,1H2,(H2,11,12,13)/t2-,3+,4+,5-,6-/m1/s1

IUPAC InChI key

HXXFSFRBOHSIMQ-FPRJBGLDSA-N
GL1

wwPDB Information

Atom count

29 (16 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

Yes

Standard parent

GLA

Defined at

2005-04-14

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



GL1 : Atoms of Molecule

Total Number of Atoms: 29
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 0.101 -0.506 0.672
2 C2 C C2 R N N 0 -1.034 -1.522 0.526
3 C3 C C3 S N N 0 -1.905 -1.13 -0.672
4 C4 C C4 R N N 0 -2.352 0.326 -0.496
5 C5 C C5 R N N 0 -1.118 1.203 -0.274
6 C6 C C6 N N N 0 -1.551 2.664 -0.132
7 H1 H H1 N N N 0 0.739 -0.792 1.508
8 H1P H H1P N N N 0 2.979 -2.082 0.278
9 H2 H H2 N N N 0 -1.639 -1.525 1.432
10 H2P H H2P N N N 0 4.173 0.298 -1.133
11 H3 H H3 N N N 0 -1.329 -1.228 -1.592
12 H4 H H4 N N N 0 -2.878 0.657 -1.392
13 H5 H H5 N N N 0 -0.446 1.105 -1.127
14 H61 H H61 N N N 0 -2.15 2.779 0.771
15 H62 H H62 N N N 0 -2.143 2.953 -1.001
16 HO2 H HO2 N N Y 0 0.06 -3.027 1.086
17 HO3 H HO3 N N Y 0 -2.721 -2.886 -0.83
18 HO4 H HO4 N N Y 0 -3.982 -0.147 0.452
19 HO6 H HO6 N N Y 0 -0.71 4.407 0.043
20 O1 O O1 N N N 0 0.874 -0.483 -0.53
21 O1P O O1P N N N 0 2.992 -1.274 0.81
22 O2 O O2 N N N 0 -0.484 -2.824 0.314
23 O2P O O2P N N N 0 3.281 0.071 -1.43
24 O3 O O3 N N N 0 -3.051 -1.982 -0.732
25 O3P O O3P N N N 0 2.373 1.167 0.654
26 O4 O O4 N N N 0 -3.223 0.425 0.633
27 O5 O O5 N N N 0 -0.441 0.792 0.912
28 O6 O O6 N N N 0 -0.393 3.497 -0.045
29 P P P N N N 0 2.38 -0.102 -0.107



GL1 : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 O2 C O sing 1.43 N N
7 C2 H2 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 O3 C O sing 1.43 N N
10 C3 H3 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 O5 C O sing 1.43 N N
16 C5 H5 C H sing 1.09 N N
17 C6 O6 C O sing 1.43 N N
18 C6 H61 C H sing 1.09 N N
19 C6 H62 C H sing 1.09 N N
20 O1 P O P sing 1.61 N N
21 O2 HO2 O H sing 0.97 N N
22 O3 HO3 O H sing 0.97 N N
23 O4 HO4 O H sing 0.97 N N
24 O6 HO6 O H sing 0.97 N N
25 P O1P P O sing 1.61 N N
26 P O2P P O sing 1.61 N N
27 P O3P P O doub 1.48 N N
28 O1P H1P O H sing 0.97 N N
29 O2P H2P O H sing 0.97 N N



GL1 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
GL1 1z4n Open in New Window Bound ligand 2 1
GL1 1z4o Open in New Window Bound ligand 2 1