Chemical Components in the PDB

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YVR : Summary

Code

YVR

One-letter code

X

Molecule name

gamma-Valerolactone

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (5~{S})-5-methyloxolan-2-one

Formula

C5 H8 O2

Formal charge

0

Molecular weight

100.116 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1CCC(=O)O1
SMILES OpenEye OEToolkits 2.0.6 CC1CCC(=O)O1
Canonical SMILES CACTVS 3.385 C[C@H]1CCC(=O)O1
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@H]1CCC(=O)O1

IUPAC InChI

InChI=1S/C5H8O2/c1-4-2-3-5(6)7-4/h4H,2-3H2,1H3/t4-/m0/s1

IUPAC InChI key

GAEKPEKOJKCEMS-BYPYZUCNSA-N
YVR

wwPDB Information

Atom count

15 (7 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-12-03

Last modified at

2017-04-28

Status

Released

Obsoleted

Not Assigned



YVR : Atoms of Molecule

Total Number of Atoms: 15
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O6 O O1 N N N 0 2.147 0.671 -0.344
2 C5 C C1 N N N 0 1.11 0.179 0.031
3 O1 O O2 N N N 0 0.055 0.85 0.514
4 C4 C C2 N N N 0 0.78 -1.302 0.028
5 C3 C C3 N N N 0 -0.758 -1.316 -0.136
6 H2 H H2 N N N 0 1.071 -1.767 0.97
7 C2 C C4 S N N 0 -1.16 0.057 0.442
8 C7 C C5 N N N 0 -2.172 0.731 -0.486
9 H1 H H1 N N N 0 1.262 -1.799 -0.813
10 H3 H H3 N N N 0 -1.036 -1.394 -1.187
11 H4 H H4 N N N 0 -1.203 -2.124 0.445
12 H5 H H5 N N N 0 -1.588 -0.062 1.438
13 H6 H H6 N N N 0 -1.735 0.846 -1.478
14 H7 H H7 N N N 0 -3.07 0.116 -0.554
15 H8 H H8 N N N 0 -2.433 1.712 -0.088



YVR : Chemical Bonds

Total Number of Bonds: 15
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 C2 C C sing 1.53 N N
2 C4 C3 C C sing 1.55 N N
3 C4 C5 C C sing 1.52 N N
4 C3 C2 C C sing 1.54 N N
5 C5 O1 C O sing 1.34 N N
6 C5 O6 C O doub 1.21 N N
7 O1 C2 O C sing 1.45 N N
8 C4 H1 C H sing 1.09 N N
9 C4 H2 C H sing 1.09 N N
10 C3 H3 C H sing 1.09 N N
11 C3 H4 C H sing 1.09 N N
12 C2 H5 C H sing 1.09 N N
13 C7 H6 C H sing 1.09 N N
14 C7 H7 C H sing 1.09 N N
15 C7 H8 C H sing 1.09 N N



YVR : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
YVR 5mg9 Open in New Window Bound ligand 1 1
YVR 7qu5 Open in New Window Bound ligand 2 1
YVR 8dk0 Open in New Window Bound ligand 1 1