Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

XH5 : Summary

Code

XH5

One-letter code

X

Molecule name

(5S)-5-methyl-1,3-diazinane-2,4-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 (5S)-5-methyl-1,3-diazinane-2,4-dione
OpenEye OEToolkits 2.0.7 (5~{S})-5-methyl-1,3-diazinane-2,4-dione

Formula

C5 H8 N2 O2

Formal charge

0

Molecular weight

128.129 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NC(=O)C(C)CN1
SMILES CACTVS 3.385 C[CH]1CNC(=O)NC1=O
SMILES OpenEye OEToolkits 2.0.7 CC1CNC(=O)NC1=O
Canonical SMILES CACTVS 3.385 C[C@H]1CNC(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H]1CNC(=O)NC1=O

IUPAC InChI

InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)/t3-/m0/s1

IUPAC InChI key

NBAKTGXDIBVZOO-VKHMYHEASA-N
XH5

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

2022-11-16

Last modified at

2023-01-27

Status

Released

Obsoleted

Not Assigned



XH5 : 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 -1.541 0.058 0.013
2 C05 C C2 N N N 0 0.664 0.837 -0.064
3 C07 C C3 S N N 0 1.154 -0.542 -0.427
4 C08 C C4 N N N 0 2.591 -0.721 0.068
5 C09 C C5 N N N 0 0.252 -1.587 0.234
6 N01 N N1 N N N 0 -1.151 -1.227 0.019
7 N04 N N2 N N N 0 -0.653 1.063 0.09
8 O03 O O1 N N N 0 -2.726 0.318 -0.069
9 O06 O O2 N N N 0 1.457 1.742 0.088
10 H1 H H1 N N N 0 1.124 -0.667 -1.51
11 H2 H H2 N N N 0 2.62 -0.599 1.151
12 H3 H H3 N N N 0 2.944 -1.718 -0.195
13 H4 H H4 N N N 0 3.232 0.026 -0.4
14 H5 H H5 N N N 0 0.447 -2.566 -0.204
15 H6 H H6 N N N 0 -0.966 1.965 0.26
16 H7 H H7 N N N 0 0.458 -1.62 1.304
17 H8 H H8 N N N 0 -1.808 -1.927 -0.121



XH5 : 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 O03 C02 O C doub 1.22 N N
2 C02 N01 C N sing 1.34 N N
3 C02 N04 C N sing 1.34 N N
4 N01 C09 N C sing 1.46 N N
5 N04 C05 N C sing 1.35 N N
6 C09 C07 C C sing 1.53 N N
7 C05 C07 C C sing 1.51 N N
8 C05 O06 C O doub 1.21 N N
9 C07 C08 C C sing 1.53 N N
10 C07 H1 C H sing 1.09 N N
11 C08 H2 C H sing 1.09 N N
12 C08 H3 C H sing 1.09 N N
13 C08 H4 C H sing 1.09 N N
14 C09 H5 C H sing 1.09 N N
15 N04 H6 N H sing 0.97 N N
16 C09 H7 C H sing 1.09 N N
17 N01 H8 N H sing 0.97 N N



XH5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XH5 8f61 Open in New Window Bound ligand 2 1