Chemical Components in the PDB

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CR5 : Summary

Code

CR5

One-letter code

G

Molecule name

(2R)-2-(AMINOMETHYL)-2,4-DIHYDROXY-5-OXO-3-(2-OXOETHYL)-2,5-DIHYDRO-1H-IMIDAZOL-3-IUM

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R)-2-(aminomethyl)-3-(carboxymethyl)-2,4-dihydroxy-5-oxo-2,5-dihydro-1H-imidazol-3-ium
OpenEye OEToolkits 1.5.0 2-[(2R)-2-(aminomethyl)-2,5-dihydroxy-4-oxo-3H-imidazol-1-ium-1-yl]ethanoic acid

Formula

C6 H10 N3 O5

Formal charge

1

Molecular weight

204.161 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C(O)=[N+](CC(=O)O)C(O)(N1)CN
SMILES CACTVS 3.341 NC[C]1(O)NC(=O)C(=[N+]1CC(O)=O)O
SMILES OpenEye OEToolkits 1.5.0 C(C(=O)O)[N+]1=C(C(=O)NC1(CN)O)O
Canonical SMILES CACTVS 3.341 NC[C@@]1(O)NC(=O)C(=[N+]1CC(O)=O)O
Canonical SMILES OpenEye OEToolkits 1.5.0 C(C(=O)O)[N+]1=C(C(=O)N[C@@]1(CN)O)O

IUPAC InChI

InChI=1S/C6H9N3O5/c7-2-6(14)8-4(12)5(13)9(6)1-3(10)11/h14H,1-2,7H2,(H2,8,10,11,12)/p+1/t6-/m1/s1

IUPAC InChI key

IMYOMVNQPPPJHU-ZCFIWIBFSA-O
CR5

wwPDB Information

Atom count

24 (14 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

GLY

Defined at

2003-09-22

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



CR5 : Atoms of Molecule

Total Number of Atoms: 24
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N N N N 0 -1.425 0.798 -1.212
2 CA1 C CA1 N N N 0 -0.415 0.988 -0.227
3 C1 C C1 R N N 0 -1.012 1.667 1.003
4 N2 N N2 N N N 0 -2.082 0.851 1.567
5 N3 N N3 N N N 1 0.022 1.681 2.1
6 C2 C C2 N N N 0 -0.415 0.978 3.074
7 O2 O O2 N N N 0 0.24 0.769 4.196
8 CA2 C CA2 N N N 0 -1.764 0.39 2.827
9 CA3 C CA3 N N N 0 1.269 2.452 2.0
10 C3 C C N N N 0 1.033 3.856 2.532
11 O3 O O3 N N N 0 2.052 4.48 2.428
12 O4 O O4 N N N 0 -1.565 2.918 0.613
13 O5 O O5 N N N 0 -2.356 -0.307 3.618
14 OXT O OXT N N Y 0 0.633 3.789 3.895
15 H H HN1 N N N 0 -2.019 1.574 -1.484
16 H2 H HN2A N N Y 0 -1.688 -0.142 -1.492
17 HA1 H HA11 N N N 0 -0.015 0.026 0.067
18 HA2 H HA12 N N N 0 0.367 1.617 -0.632
19 HN2 H HN2 N N N 0 -2.954 0.648 1.09
20 HO2 H HO2 N N N 0 -0.326 0.847 4.999
21 HA31 H HA31 N N N 0 1.556 2.453 0.944
22 HA32 H HA32 N N N 0 2.023 1.911 2.581
23 HO4 H HO4 N N N 0 -1.209 3.118 -0.267
24 HXT H HXT N N Y 0 1.306 4.282 4.411



CR5 : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 CA1 N C sing 1.42 N N
2 N1 H N H sing 1.01 N N
3 N1 H2 N H sing 1.02 N N
4 CA1 C1 C C sing 1.53 N N
5 CA1 HA1 C H sing 1.08 N N
6 CA1 HA2 C H sing 1.08 N N
7 C1 N2 C N sing 1.46 N N
8 C1 N3 C N sing 1.51 N N
9 C1 O4 C O sing 1.42 N N
10 N2 CA2 N C sing 1.38 N N
11 N2 HN2 N H sing 1.01 N N
12 N3 C2 N C doub 1.28 N N
13 N3 CA3 N C sing 1.47 N N
14 C2 O2 C O sing 1.32 N N
15 C2 CA2 C C sing 1.49 N N
16 O2 HO2 O H sing 0.99 N N
17 CA2 O5 C O doub 1.21 N N
18 CA3 C3 C C sing 1.52 N N
19 CA3 HA31 C H sing 1.09 N N
20 CA3 HA32 C H sing 1.09 N N
21 C3 O3 C O doub 1.2 N N
22 C3 OXT C O sing 1.42 N N
23 O4 HO4 O H sing 0.97 N N
24 OXT HXT O H sing 0.98 N N



CR5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
CR5 1qyq Open in New Window Polymer component 1 1