Chemical Components in the PDB

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X3B : Summary

Code

X3B

One-letter code

X

Molecule name

2-methylidene-1,3-dioxane-4,4-diol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-methylidene-1,3-dioxane-4,4-diol

Formula

C5 H8 O4

Formal charge

0

Molecular weight

132.115 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC1(O)CCOC(=C)O1
SMILES OpenEye OEToolkits 2.0.7 C=C1OCCC(O1)(O)O
Canonical SMILES CACTVS 3.385 OC1(O)CCOC(=C)O1
Canonical SMILES OpenEye OEToolkits 2.0.7 C=C1OCCC(O1)(O)O

IUPAC InChI

InChI=1S/C5H8O4/c1-4-8-3-2-5(6,7)9-4/h6-7H,1-3H2

IUPAC InChI key

IMDAPZFNKPSNIF-UHFFFAOYSA-N
X3B

wwPDB Information

Atom count

17 (9 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-05-31

Last modified at

2023-10-20

Status

Released

Obsoleted

Not Assigned



X3B : Atoms of Molecule

Total Number of Atoms: 17
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C1 N N N 0 -1.037 0.127 0.018
2 C04 C C2 N N N 0 1.291 0.488 0.224
3 C06 C C3 N N N 0 0.615 -1.714 -0.308
4 C07 C C4 N N N 0 -0.769 -1.364 0.252
5 C08 C C5 N N N 0 2.194 1.37 -0.182
6 O01 O O1 N N N 0 -1.11 0.387 -1.385
7 H1 H H1 N N N 0 0.856 -2.749 -0.066
8 O03 O O2 N N N 0 0.039 0.883 0.592
9 O05 O O3 N N N 0 1.585 -0.842 0.286
10 O09 O O4 N N N 0 -2.268 0.497 0.641
11 H5 H H5 N N N 0 3.181 1.038 -0.47
12 H2 H H2 N N N 0 0.618 -1.582 -1.39
13 H3 H H3 N N N 0 -0.795 -1.576 1.32
14 H4 H H4 N N N 0 -1.529 -1.956 -0.258
15 H6 H H6 N N N 0 1.943 2.419 -0.225
16 H7 H H7 N N N 0 -1.277 1.314 -1.606
17 H8 H H8 N N N 0 -2.5 1.429 0.533



X3B : Chemical Bonds

Total Number of Bonds: 17
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O09 C02 O C sing 1.43 N N
2 O01 C02 O C sing 1.43 N N
3 C02 C07 C C sing 1.53 N N
4 C02 O03 C O sing 1.43 N N
5 C07 C06 C C sing 1.53 N N
6 O03 C04 O C sing 1.36 N N
7 C06 O05 C O sing 1.43 N N
8 C04 C08 C C doub 1.33 N N
9 C04 O05 C O sing 1.36 N N
10 C06 H1 C H sing 1.09 N N
11 C06 H2 C H sing 1.09 N N
12 C07 H3 C H sing 1.09 N N
13 C07 H4 C H sing 1.09 N N
14 C08 H5 C H sing 1.08 N N
15 C08 H6 C H sing 1.08 N N
16 O01 H7 O H sing 0.97 N N
17 O09 H8 O H sing 0.97 N N



X3B : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X3B 8p7h Open in New Window Bound ligand 1 1