Chemical Components in the PDB

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H3M : Summary

Code

H3M

One-letter code

X

Molecule name

(5R)-5-hydroxy-3-methylfuran-2(5H)-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (5R)-5-hydroxy-3-methylfuran-2(5H)-one
OpenEye OEToolkits 1.7.6 (2R)-4-methyl-2-oxidanyl-2H-furan-5-one

Formula

C5 H6 O3

Formal charge

0

Molecular weight

114.099 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1OC(O)C=C1C
SMILES CACTVS 3.370 CC1=C[CH](O)OC1=O
SMILES OpenEye OEToolkits 1.7.6 CC1=CC(OC1=O)O
Canonical SMILES CACTVS 3.370 CC1=C[C@H](O)OC1=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC1=C[C@@H](OC1=O)O

IUPAC InChI

InChI=1S/C5H6O3/c1-3-2-4(6)8-5(3)7/h2,4,6H,1H3/t4-/m1/s1

IUPAC InChI key

HQIZYPQNJWENRT-SCSAIBSYSA-N
H3M

wwPDB Information

Atom count

14 (8 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-10-02

Last modified at

2013-10-18

Status

Released

Obsoleted

Not Assigned



H3M : Atoms of Molecule

Total Number of Atoms: 14
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -0.639 0.792 -0.021
2 C2 C C2 R N N 0 1.375 -0.15 -0.431
3 C3 C C3 N N N 0 0.351 -1.251 -0.281
4 C4 C C4 N N N 0 -0.818 -0.663 -0.042
5 C5 C C5 N N N 0 -2.125 -1.381 0.174
6 H2 H H2 N N N 0 -2.916 -0.652 0.348
7 H3 H H3 N N N 0 -2.365 -1.973 -0.709
8 H4 H H4 N N N 0 -2.04 -2.038 1.039
9 H5 H H5 N N N 0 0.533 -2.313 -0.354
10 H7 H H7 N N N 0 1.822 -0.186 -1.424
11 H8 H H8 N N N 0 3.075 0.397 0.524
12 O1 O O1 N N N 0 -1.525 1.601 0.174
13 O2 O O2 N N N 0 0.65 1.099 -0.255
14 O3 O O3 N N N 0 2.388 -0.282 0.568



H3M : Chemical Bonds

Total Number of Bonds: 14
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 C4 C C sing 1.51 N N
2 C3 C4 C C doub 1.33 N N
3 C3 C2 C C sing 1.51 N N
4 C4 C1 C C sing 1.47 N N
5 C2 O3 C O sing 1.43 N N
6 C2 O2 C O sing 1.45 N N
7 C1 O1 C O doub 1.22 N N
8 C1 O2 C O sing 1.35 N N
9 C5 H2 C H sing 1.09 N N
10 C5 H3 C H sing 1.09 N N
11 C5 H4 C H sing 1.09 N N
12 C3 H5 C H sing 1.08 N N
13 C2 H7 C H sing 1.09 N N
14 O3 H8 O H sing 0.97 N N



H3M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
H3M 3wio Open in New Window Bound ligand 1 1