Chemical Components in the PDB

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GDE : Summary

Code

GDE

One-letter code

X

Molecule name

3,4,5-trihydroxybenzoic acid

Synonyms

Gallate

Systematic names

ProgramVersionName
ACDLabs 12.01 3,4,5-trihydroxybenzoic acid
OpenEye OEToolkits 1.7.2 3,4,5-tris(oxidanyl)benzoic acid

Formula

C7 H6 O5

Formal charge

0

Molecular weight

170.12 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)c1cc(O)c(O)c(O)c1
SMILES CACTVS 3.370 OC(=O)c1cc(O)c(O)c(O)c1
SMILES OpenEye OEToolkits 1.7.2 c1c(cc(c(c1O)O)O)C(=O)O
Canonical SMILES CACTVS 3.370 OC(=O)c1cc(O)c(O)c(O)c1
Canonical SMILES OpenEye OEToolkits 1.7.2 c1c(cc(c(c1O)O)O)C(=O)O

IUPAC InChI

InChI=1S/C7H6O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1-2,8-10H,(H,11,12)

IUPAC InChI key

LNTHITQWFMADLM-UHFFFAOYSA-N
GDE

wwPDB Information

Atom count

18 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-11-08

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



GDE : Atoms of Molecule

Total Number of Atoms: 18
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAA O OAA N N N 0 3.219 1.065 0.025
2 OAB O OAB N N N 0 3.094 -1.151 -0.0090
3 OAC O OAC N N N 0 -1.785 -2.354 -0.049
4 OAD O OAD N N N 0 -1.66 2.41 0.025
5 OAE O OAE N N N 0 -3.094 0.064 -0.017
6 CAF C CAF N Y N 0 0.309 -1.235 -0.023
7 CAG C CAG N Y N 0 0.372 1.183 0.014
8 CAH C CAH N N N 0 2.515 -0.084 0.0040
9 CAI C CAI N Y N 0 -1.073 -1.196 -0.028
10 CAJ C CAJ N Y N 0 -1.009 1.216 0.0090
11 CAK C CAK N Y N 0 1.04 -0.045 -0.0020
12 CAL C CAL N Y N 0 -1.736 0.029 -0.012
13 HOAA H HOAA N N N 0 4.183 0.989 0.028
14 HOAC H HOAC N N N 0 -1.995 -2.703 0.828
15 HOAD H HOAD N N N 0 -1.844 2.77 -0.854
16 HOAE H HOAE N N N 0 -3.491 0.061 0.864
17 HAF H HAF N N N 0 0.822 -2.185 -0.031
18 HAG H HAG N N N 0 0.935 2.104 0.03



GDE : Chemical Bonds

Total Number of Bonds: 18
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAA CAH O C sing 1.35 N N
2 OAB CAH O C doub 1.21 N N
3 OAC CAI O C sing 1.36 N N
4 OAD CAJ O C sing 1.36 N N
5 OAE CAL O C sing 1.36 N N
6 CAF CAI C C doub 1.38 N Y
7 CAF CAK C C sing 1.4 N Y
8 CAG CAJ C C sing 1.38 N Y
9 CAG CAK C C doub 1.4 N Y
10 CAH CAK C C sing 1.48 N N
11 CAI CAL C C sing 1.39 N Y
12 CAJ CAL C C doub 1.39 N Y
13 OAA HOAA O H sing 0.97 N N
14 OAC HOAC O H sing 0.97 N N
15 OAD HOAD O H sing 0.97 N N
16 OAE HOAE O H sing 0.97 N N
17 CAF HAF C H sing 1.08 N N
18 CAG HAG C H sing 1.08 N N



GDE : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
GDE 3wku Open in New Window Bound ligand 1 1
GDE 3wpm Open in New Window Bound ligand 1 1
GDE 3wr3 Open in New Window Bound ligand 1 1
GDE 3wr4 Open in New Window Bound ligand 1 1
GDE 3wr9 Open in New Window Bound ligand 2 1
GDE 3wrb Open in New Window Bound ligand 2 1
GDE 4ic0 Open in New Window Bound ligand 2 1
GDE 4j0h Open in New Window Bound ligand 2 1
GDE 4z5x Open in New Window Bound ligand 1 1
GDE 7k4o Open in New Window Bound ligand 1 1