Chemical Components in the PDB

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2AL : Summary

Code

2AL

One-letter code

X

Molecule name

1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA

Systematic names

ProgramVersionName
ACDLabs 10.04 1-(2,5-dioxo-2,5-dihydro-1H-imidazol-4-yl)urea
OpenEye OEToolkits 1.5.0 (2,5-dioxoimidazol-4-yl)urea

Formula

C4 H4 N4 O3

Formal charge

0

Molecular weight

156.1 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C(=NC(=O)N1)NC(=O)N
SMILES CACTVS 3.341 NC(=O)NC1=NC(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 C1(=O)C(=NC(=O)N1)NC(=O)N
Canonical SMILES CACTVS 3.341 NC(=O)NC1=NC(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1(=O)C(=NC(=O)N1)NC(=O)N

IUPAC InChI

InChI=1S/C4H4N4O3/c5-3(10)6-1-2(9)8-4(11)7-1/h(H4,5,6,7,8,9,10,11)

IUPAC InChI key

MFAONEQLPARJAO-UHFFFAOYSA-N
2AL

wwPDB Information

Atom count

15 (11 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-02-07

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



2AL : 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 C4 C C4 N N N 0 -0.008 -0.326 0.002
2 C5 C C5 N N N 0 -1.22 -1.206 -0.002
3 O5 O O5 N N N 0 -1.249 -2.418 -0.002
4 N7 N N7 N N N 0 -2.274 -0.36 0.003
5 C8 C C8 N N N 0 -1.799 0.898 0.001
6 O8 O O8 N N N 0 -2.494 1.895 -0.001
7 N9 N N9 N N N 0 -0.457 0.907 0.0
8 N3 N N3 N N N 0 1.302 -0.727 0.002
9 C2 C C2 N N N 0 2.288 0.192 0.0
10 N1 N N1 N N N 0 3.577 -0.202 0.0
11 O2 O O2 N N N 0 2.014 1.377 -0.001
12 HN7 H HN7 N N N 0 -3.21 -0.616 0.003
13 HN3 H HN3 N N N 0 1.52 -1.672 0.003
14 HN11 H 1HN1 N N N 0 4.286 0.46 -0.002
15 HN12 H 2HN1 N N N 0 3.795 -1.147 0.005



2AL : 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 C4 C5 C C sing 1.5 N N
2 C4 N9 C N doub 1.31 N N
3 C4 N3 C N sing 1.37 N N
4 C5 O5 C O doub 1.21 N N
5 C5 N7 C N sing 1.35 N N
6 N7 C8 N C sing 1.34 N N
7 N7 HN7 N H sing 0.97 N N
8 C8 O8 C O doub 1.22 N N
9 C8 N9 C N sing 1.34 N N
10 N3 C2 N C sing 1.35 N N
11 N3 HN3 N H sing 0.97 N N
12 C2 N1 C N sing 1.35 N N
13 C2 O2 C O doub 1.22 N N
14 N1 HN11 N H sing 0.97 N N
15 N1 HN12 N H sing 0.97 N N



2AL : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
2AL 2fxl Open in New Window Bound ligand 1 1
2AL 2o73 Open in New Window Bound ligand 6 1
2AL 3o7j Open in New Window Bound ligand 1 1
2AL 3qvk Open in New Window Bound ligand 2 1