Chemical Components in the PDB

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BDP : Summary

Code

BDP

One-letter code

X

Molecule name

beta-D-glucopyranuronic acid

Synonyms

beta-D-glucuronic acid
D-glucuronic acid
glucuronic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 beta-D-glucopyranuronic acid
OpenEye OEToolkits 1.7.0 (2S,3S,4S,5R,6R)-3,4,5,6-tetrahydroxyoxane-2-carboxylic acid

Formula

C6 H10 O7

Formal charge

0

Molecular weight

194.139 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C1OC(O)C(O)C(O)C1O
SMILES CACTVS 3.370 O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(O)=O
SMILES OpenEye OEToolkits 1.7.0 C1(C(C(OC(C1O)O)C(=O)O)O)O
Canonical SMILES CACTVS 3.370 O[C@@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 [C@@H]1([C@@H]([C@H](O[C@H]([C@@H]1O)O)C(=O)O)O)O

IUPAC InChI

InChI=1S/C6H10O7/c7-1-2(8)4(5(10)11)13-6(12)3(1)9/h1-4,6-9,12H,(H,10,11)/t1-,2-,3+,4-,6+/m0/s1

IUPAC InChI key

AEMOLEFTQBMNLQ-QIUUJYRFSA-N

Is part of

NTO
BDP

wwPDB Information

Atom count

23 (13 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, beta linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2001-11-26

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



BDP : 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 -1.248 1.252 0.387
2 C2 C C2 R N N 0 -1.851 -0.001 -0.255
3 C3 C C3 S N N 0 -1.037 -1.226 0.173
4 C4 C C4 S N N 0 0.427 -1.017 -0.224
5 C5 C C5 S N N 0 0.942 0.275 0.417
6 C6 C C6 N N N 0 2.364 0.519 -0.016
7 O2 O O2 N N N 0 -3.205 -0.153 0.174
8 O3 O O3 N N N 0 -1.548 -2.39 -0.48
9 O4 O O4 N N N 0 1.209 -2.121 0.235
10 O5 O O5 N N N 0 0.123 1.37 0.002
11 O6A O O6A N N N 0 2.632 1.482 -0.695
12 O1 O O1 N N Y 0 -1.968 2.406 -0.053
13 O6B O O6B N N N 0 3.334 -0.333 0.352
14 H1 H H1 N N N 0 -1.316 1.173 1.472
15 H2 H H2 N N N 0 -1.82 0.096 -1.341
16 H3 H H3 N N N 0 -1.108 -1.351 1.253
17 H4 H H4 N N N 0 0.504 -0.941 -1.308
18 H5 H H5 N N N 0 0.903 0.183 1.503
19 HO2 H HB N N Y 0 -3.778 0.591 -0.06
20 HO3 H HC N N Y 0 -2.474 -2.579 -0.279
21 HO4 H HD N N Y 0 2.149 -2.055 0.018
22 HO1 H HA N N Y 0 -1.64 3.237 0.315
23 HO6B H H6B N N N 0 4.231 -0.135 0.05



BDP : 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 C1 C2 C C sing 1.53 N N
2 C1 O5 C O sing 1.43 N N
3 C1 O1 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 1.51 N N
15 C5 O5 C O sing 1.43 N N
16 C5 H5 C H sing 1.09 N N
17 C6 O6A C O doub 1.21 N N
18 C6 O6B C O sing 1.34 N N
19 O2 HO2 O H sing 0.97 N N
20 O3 HO3 O H sing 0.97 N N
21 O4 HO4 O H sing 0.97 N N
22 O1 HO1 O H sing 0.97 N N
23 O6B HO6B O H sing 0.97 N N



BDP : Used in PDB Entries

Total Number of PDB Entries: 90
Ligand Code PDB Entry ID Type Total Distinct
BDP 1cap Open in New Window s 2 2
BDP 1gqk Open in New Window Bound ligand 2 1
BDP 1gql Open in New Window Bound ligand 2 1
BDP 1hm3 Open in New Window s 1 1
BDP 1hmw Open in New Window s 1 1
BDP 1hua Open in New Window s 1 1
BDP 1loh Open in New Window s 3 3
BDP 1lxk Open in New Window s 2 2
BDP 1lxm Open in New Window s 3 3
BDP 1n7q Open in New Window s 2 2
BDP 1n7r Open in New Window s 3 3
BDP 1ofm Open in New Window s 1 1
BDP 1on8 Open in New Window s 2 1
BDP 2bvk Open in New Window s 4 4
BDP 2gd4 Open in New Window s 2 1
BDP 2jcq Open in New Window s 3 3
BDP 2jcr Open in New Window s 3 3
BDP 2kqo Open in New Window s 3 3
BDP 3a0n Open in New Window Bound ligand 1 1
BDP 3c9e Open in New Window s 3 3
BDP 3evj Open in New Window s 2 1
BDP 3h7d Open in New Window s 3 3
BDP 3hya Open in New Window s 3 3
BDP 3im0 Open in New Window Bound ligand 1 1
BDP 3kl3 Open in New Window Bound ligand 1 1
BDP 3uan Open in New Window Bound ligand 1 1
BDP 3uug Open in New Window Bound ligand 2 1
BDP 3vnz Open in New Window Bound ligand 1 1
BDP 4c4m Open in New Window s 2 2
BDP 4fms Open in New Window Bound ligand 2 1
BDP 4mhf Open in New Window Bound ligand 1 1
BDP 4mrd Open in New Window s 2 2
BDP 4n15 Open in New Window Bound ligand 1 1
BDP 4n8w Open in New Window s 3 3
BDP 4n91 Open in New Window Bound ligand 1 1
BDP 4ndz Open in New Window s 15 3
BDP 4ovq Open in New Window Bound ligand 1 1
BDP 4p1l Open in New Window Bound ligand 2 1
BDP 4p3l Open in New Window Bound ligand 1 1
BDP 4qb2 Open in New Window Bound ligand 1 1
BDP 4r9w Open in New Window s 1 1
BDP 4x04 Open in New Window Bound ligand 4 1
BDP 4x7r Open in New Window s 2 1
BDP 4x8r Open in New Window Bound ligand 2 1
BDP 4xfe Open in New Window Bound ligand 1 1
BDP 5e97 Open in New Window s 2 2
BDP 5e98 Open in New Window s 2 2
BDP 5e9b Open in New Window s 2 2
BDP 5ik5 Open in New Window s 2 2
BDP 5ik8 Open in New Window s 2 2
BDP 5mul Open in New Window Bound ligand 1 1
BDP 5t03 Open in New Window s 6 3
BDP 5t05 Open in New Window s 4 2
BDP 5t0a Open in New Window s 5 5
BDP 5uas Open in New Window s 2 1
BDP 5uf6 Open in New Window s 1 1
BDP 5wd7 Open in New Window s 1 1
BDP 5z1b Open in New Window Bound ligand 4 1
BDP 6bjq Open in New Window Bound ligand 1 1
BDP 6byt Open in New Window s 2 1
BDP 6byx Open in New Window s 2 1
BDP 6d3u Open in New Window s 2 1
BDP 6e0w Open in New Window s 2 1
BDP 6euf Open in New Window s 4 2
BDP 6i01 Open in New Window s 8 4
BDP 6jz5 Open in New Window Bound ligand 2 1
BDP 6s21 Open in New Window s 3 1
BDP 6syv Open in New Window Bound ligand 1 1
BDP 6sz4 Open in New Window Bound ligand 1 1
BDP 6wwx Open in New Window s 6 1
BDP 6wxa Open in New Window s 8 5
BDP 6x3m Open in New Window s 36 4
BDP 6xkg Open in New Window s 3 3
BDP 6xl8 Open in New Window s 3 3
BDP 7ctm Open in New Window Bound ligand 1 1
BDP 7dfs Open in New Window s 1 1
BDP 7esn Open in New Window s 1 1
BDP 7fap Open in New Window s 6 6
BDP 7jgh Open in New Window s 6 6
BDP 7jvd Open in New Window s 1 1
BDP 7puy Open in New Window s 3 1
BDP 7pvd Open in New Window s 6 6
BDP 7qe2 Open in New Window Bound ligand 2 1
BDP 7qee Open in New Window Bound ligand 1 1
BDP 7qrn Open in New Window s 1 1
BDP 7scd Open in New Window s 3 3
BDP 7sce Open in New Window s 2 2
BDP 7scj Open in New Window s 1 1
BDP 7sck Open in New Window s 2 2
BDP 8get Open in New Window Bound ligand 3 1