Chemical Components in the PDB

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3GR : Summary

Code

3GR

One-letter code

X

Molecule name

D-Glyceraldehyde

Synonyms

GLYCERALDEHYDE
(2R)-2,3-DIHYDROXYPROPANAL

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R)-2,3-dihydroxypropanal
OpenEye OEToolkits 2.0.7 (2~{R})-2,3-bis(oxidanyl)propanal

Formula

C3 H6 O3

Formal charge

0

Molecular weight

90.078 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(O)C(O)C=O
SMILES CACTVS 3.385 OC[CH](O)C=O
SMILES OpenEye OEToolkits 2.0.7 C(C(C=O)O)O
Canonical SMILES CACTVS 3.385 OC[C@@H](O)C=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C([C@H](C=O)O)O

IUPAC InChI

InChI=1S/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/m0/s1

IUPAC InChI key

MNQZXJOMYWMBOU-VKHMYHEASA-N
3GR

wwPDB Information

Atom count

12 (6 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2004-07-19

Last modified at

2020-06-29

Status

Released

Obsoleted

Not Assigned



3GR : Atoms of Molecule

Total Number of Atoms: 12
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C3 C C1 N N N 0 -1.103 -0.671 0.297
2 O3 O O1 N N N 0 -2.35 -0.047 -0.015
3 C2 C C2 R N N 0 0.023 0.03 -0.466
4 O2 O O2 N N N 0 0.146 1.376 -0.0030
5 C1 C C3 N N N 0 1.319 -0.702 -0.234
6 O1 O O3 N N N 0 2.253 -0.131 0.276
7 H31 H H31 N N N 0 -0.917 -0.595 1.369
8 H32 H H32 N N N 0 -1.139 -1.721 0.0080
9 HO3 H H1 N N N 0 -3.11 -0.441 0.435
10 H2 H H2 N N N 0 -0.208 0.032 -1.532
11 HO2 H HA N N N 0 0.351 1.45 0.939
12 H1 H H3 N N N 0 1.413 -1.739 -0.524



3GR : Chemical Bonds

Total Number of Bonds: 11
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3 O3 C O sing 1.43 N N
2 C3 C2 C C sing 1.53 N N
3 C3 H31 C H sing 1.09 N N
4 C3 H32 C H sing 1.09 N N
5 O3 HO3 O H sing 0.97 N N
6 C2 O2 C O sing 1.43 N N
7 C2 C1 C C sing 1.51 N N
8 C2 H2 C H sing 1.09 N N
9 O2 HO2 O H sing 0.97 N N
10 C1 O1 C O doub 1.21 N N
11 C1 H1 C H sing 1.08 N N



3GR : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
3GR 1t5e Open in New Window Bound ligand 9 1
3GR 1w3t Open in New Window Bound ligand 4 1
3GR 3kwm Open in New Window Bound ligand 1 1
3GR 3v36 Open in New Window Bound ligand 1 1
3GR 4b5s Open in New Window Bound ligand 1 1
3GR 5tg4 Open in New Window Bound ligand 2 1