Chemical Components in the PDB

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GMH : Summary

Code

GMH

One-letter code

X

Molecule name

L-glycero-alpha-D-manno-heptopyranose

Systematic names

ProgramVersionName
ACDLabs 10.04 L-glycero-alpha-D-manno-heptopyranose
OpenEye OEToolkits 1.5.0 (2S,3S,4S,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]oxane-2,3,4,5-tetrol

Formula

C7 H14 O7

Formal charge

0

Molecular weight

210.182 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(O)C(OC(O)C1O)C(O)CO
SMILES CACTVS 3.341 OC[CH](O)[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C(C(C1C(C(C(C(O1)O)O)O)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@H](O)[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O)O

IUPAC InChI

InChI=1S/C7H14O7/c8-1-2(9)6-4(11)3(10)5(12)7(13)14-6/h2-13H,1H2/t2-,3-,4-,5-,6+,7-/m0/s1

IUPAC InChI key

BGWQRWREUZVRGI-QQABCQGCSA-N
GMH

wwPDB Information

Atom count

28 (14 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



GMH : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 1.729 0.015 -0.981
2 C2 C C2 S N N 0 0.783 -0.269 -2.149
3 C3 C C3 S N N 0 -0.529 0.488 -1.925
4 C4 C C4 S N N 0 -1.075 0.123 -0.54
5 C5 C C5 R N N 0 0.01 0.379 0.506
6 C6 C C6 S N N 0 -0.535 0.051 1.897
7 C7 C C7 N N N 0 0.548 0.311 2.945
8 O1 O O1 N N Y 0 1.965 1.422 -0.895
9 O2 O O2 N N N 0 0.521 -1.672 -2.221
10 O3 O O3 N N N 0 -1.475 0.116 -2.93
11 O4 O O4 N N N 0 -2.219 0.928 -0.249
12 O5 O O5 N N N 0 1.144 -0.442 0.236
13 O6 O O6 N N N 0 -0.924 -1.322 1.944
14 O7 O O7 N N N 0 0.037 0.004 4.244
15 H1 H H1 N N N 0 2.675 -0.501 -1.145
16 H2 H H2 N N N 0 1.243 0.063 -3.08
17 H3 H H3 N N N 0 -0.345 1.561 -1.976
18 H4 H H4 N N N 0 -1.356 -0.929 -0.525
19 H5 H H5 N N N 0 0.307 1.428 0.471
20 H6 H H6 N N N 0 -1.4 0.681 2.105
21 H71 H H71 N N N 0 0.844 1.359 2.909
22 H72 H H72 N N N 0 1.413 -0.318 2.737
23 HO1 H HO1 N N Y 0 2.568 1.559 -0.151
24 HO2 H HO2 N N Y 0 1.373 -2.109 -2.355
25 HO3 H HO3 N N Y 0 -1.085 0.352 -3.782
26 HO4 H HO4 N N Y 0 -2.874 0.741 -0.936
27 HO6 H HO6 N N Y 0 -0.132 -1.843 1.755
28 HO7 H HO7 N N Y 0 0.75 0.181 4.874



GMH : Chemical Bonds

Total Number of Bonds: 28
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 C7 C C sing 1.53 N N
18 C6 O6 C O sing 1.43 N N
19 C6 H6 C H sing 1.09 N N
20 C7 O7 C O sing 1.43 N N
21 C7 H71 C H sing 1.09 N N
22 C7 H72 C H sing 1.09 N N
23 O1 HO1 O H sing 0.97 N N
24 O2 HO2 O H sing 0.97 N N
25 O3 HO3 O H sing 0.97 N N
26 O4 HO4 O H sing 0.97 N N
27 O6 HO6 O H sing 0.97 N N
28 O7 HO7 O H sing 0.97 N N



GMH : Used in PDB Entries

Total Number of PDB Entries: 21
Ligand Code PDB Entry ID Type Total Distinct
GMH 1fcp Open in New Window s 1 1
GMH 1fi1 Open in New Window s 3 3
GMH 1qff Open in New Window s 2 2
GMH 1qfg Open in New Window s 2 2
GMH 1qjq Open in New Window s 3 3
GMH 1qkc Open in New Window s 3 3
GMH 2fcp Open in New Window s 1 1
GMH 2grx Open in New Window s 2 1
GMH 2rib Open in New Window Bound ligand 3 1
GMH 2ric Open in New Window Bound ligand 1 1
GMH 3fxi Open in New Window s 6 6
GMH 3v0w Open in New Window s 1 1
GMH 4c83 Open in New Window s 4 2
GMH 4cu4 Open in New Window s 2 2
GMH 4e52 Open in New Window s 2 1
GMH 5fvn Open in New Window s 3 1
GMH 5oxr Open in New Window s 4 2
GMH 5oxs Open in New Window s 6 2
GMH 5tv4 Open in New Window s 3 3
GMH 6bpl Open in New Window s 3 3
GMH 6bpp Open in New Window s 3 3