Chemical Components in the PDB

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DYG : Summary

Code

DYG

One-letter code

DYG

Molecule name

(3S)-3-amino-3-[(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-2-yl]propanoic acid

Systematic names

ProgramVersionName
ACDLabs 10.04 (3S)-3-amino-3-{(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-2-yl}propanoic acid
OpenEye OEToolkits 1.5.0 (3S)-3-amino-3-[(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-2-yl]propanoic acid

Formula

C15 H15 N3 O6

Formal charge

0

Molecular weight

333.296 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)CC(N)C1=N/C(C(=O)N1CC(=O)O)=C\c2ccc(O)cc2
SMILES CACTVS 3.341 N[CH](CC(O)=O)C1=NC(=Cc2ccc(O)cc2)C(=O)N1CC(O)=O
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C=C2C(=O)N(C(=N2)C(CC(=O)O)N)CC(=O)O)O
Canonical SMILES CACTVS 3.341 N[C@@H](CC(O)=O)C1=N\C(=C/c2ccc(O)cc2)C(=O)N1CC(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1\C=C/2\C(=O)N(C(=N2)[C@H](CC(=O)O)N)CC(=O)O)O

IUPAC InChI

InChI=1S/C15H15N3O6/c16-10(6-12(20)21)14-17-11(15(24)18(14)7-13(22)23)5-8-1-3-9(19)4-2-8/h1-5,10,19H,6-7,16H2,(H,20,21)(H,22,23)/b11-5-/t10-/m0/s1

IUPAC InChI key

PGTRRWBPGBMHIF-QIMWGGGBSA-N
DYG

wwPDB Information

Atom count

39 (24 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

ASP TYR GLY

Defined at

2004-10-25

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



DYG : Atoms of Molecule

Total Number of Atoms: 39
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 0.966 2.069 -1.657
2 OD2 O OD2 N N N 0 3.446 3.588 1.35
3 OD1 O OD1 N N N 0 3.353 3.198 -0.823
4 CG1 C CG1 N N N 0 3.006 2.889 0.292
5 CB1 C CB1 N N N 0 2.08 1.718 0.495
6 CA1 C CA1 S N N 0 1.732 1.101 -0.861
7 C1 C C1 N N N 0 0.907 -0.142 -0.651
8 N2 N N2 N N N 0 -0.38 -0.147 -0.495
9 N3 N N3 N N N 0 1.418 -1.409 -0.606
10 C2 C C2 N N N 0 0.398 -2.273 -0.404
11 O2 O O2 N N N 0 0.465 -3.485 -0.308
12 CA2 C CA2 N N N 0 -0.811 -1.434 -0.329
13 CA3 C CA3 N N N 0 2.83 -1.769 -0.752
14 CB2 C CB2 N N N 0 -2.107 -1.859 -0.135
15 CG2 C CG2 N Y N 0 -3.183 -0.879 0.023
16 CD1 C CD1 N Y N 0 -4.479 -1.302 0.352
17 CD2 C CD2 N Y N 0 -2.921 0.488 -0.147
18 CE1 C CE1 N Y N 0 -5.482 -0.38 0.498
19 CE2 C CE2 N Y N 0 -3.932 1.401 0.002
20 CZ C CZ N Y N 0 -5.217 0.974 0.322
21 OH O OH N N N 0 -6.214 1.883 0.468
22 C3 C C N N N 0 3.491 -1.771 0.602
23 O3 O O N N N 0 2.848 -1.5 1.589
24 OXT O OXT N N Y 0 4.794 -2.075 0.713
25 HXT H HXT N N Y 0 5.173 -2.063 1.603
26 HA1 H HA1 N N N 0 2.651 0.842 -1.388
27 HD2 H HD2 N N N 0 4.039 4.331 1.17
28 HB11 H HB11 N N N 0 2.57 0.97 1.12
29 HB12 H HB12 N N N 0 1.167 2.057 0.985
30 H H HN1 N N N 0 0.78 1.71 -2.582
31 H2 H HN2 N N Y 0 0.11 2.325 -1.189
32 HB2 H HB2 N N N 0 -2.329 -2.916 -0.099
33 H1 H H1 N N N 0 -1.924 0.821 -0.395
34 HE2 H HE2 N N N 0 -3.732 2.454 -0.129
35 HOH H HOH N N N 0 -6.31 2.22 1.369
36 HE1 H HE1 N N N 0 -6.481 -0.705 0.751
37 HD1 H HD1 N N N 0 -4.686 -2.353 0.488
38 HA31 H HA31 N N N 0 2.908 -2.761 -1.196
39 HA32 H HA32 N N N 0 3.326 -1.042 -1.396



DYG : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 CA1 N C sing 1.47 N N
2 N1 H N H sing 1.01 N N
3 N1 H2 N H sing 1.01 N N
4 OD2 HD2 O H sing 0.97 N N
5 OD2 CG1 O C sing 1.34 N N
6 OD1 CG1 O C doub 1.21 N N
7 CG1 CB1 C C sing 1.51 N N
8 CB1 HB11 C H sing 1.09 N N
9 CB1 HB12 C H sing 1.09 N N
10 CB1 CA1 C C sing 1.53 N N
11 CA1 HA1 C H sing 1.09 N N
12 CA1 C1 C C sing 1.51 N N
13 C1 N2 C N doub 1.3 N N
14 C1 N3 C N sing 1.37 N N
15 N2 CA2 N C sing 1.37 N N
16 N3 C2 N C sing 1.35 N N
17 N3 CA3 N C sing 1.46 N N
18 C2 CA2 C C sing 1.47 N N
19 C2 O2 C O doub 1.22 N N
20 CA2 CB2 C C doub 1.38 Z N
21 CA3 HA31 C H sing 1.09 N N
22 CA3 HA32 C H sing 1.09 N N
23 CA3 C3 C C sing 1.51 N N
24 CB2 HB2 C H sing 1.08 N N
25 CB2 CG2 C C sing 1.46 N N
26 CG2 CD2 C C doub 1.4 N Y
27 CG2 CD1 C C sing 1.4 N Y
28 CD1 CE1 C C doub 1.37 N Y
29 CD1 HD1 C H sing 1.08 N N
30 CD2 H1 C H sing 1.08 N N
31 CD2 CE2 C C sing 1.37 N Y
32 CE1 CZ C C sing 1.39 N Y
33 CE1 HE1 C H sing 1.08 N N
34 CE2 HE2 C H sing 1.08 N N
35 CE2 CZ C C doub 1.39 N Y
36 CZ OH C O sing 1.36 N N
37 OH HOH O H sing 0.97 N N
38 C3 O3 C O doub 1.21 N N
39 C3 OXT C O sing 1.34 N N
40 OXT HXT O H sing 0.97 N N



DYG : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
DYG 1xss Open in New Window Polymer component 2 1
DYG 2pxs Open in New Window Polymer component 6 1
DYG 2pxw Open in New Window Polymer component 2 1