Chemical Components in the PDB

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YPZ : Summary

Code

YPZ

One-letter code

Y

Molecule name

3-[(3Z)-4-hydroxy-6-oxo-3-(2-phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]-L-alanine

Systematic names

ProgramVersionName
ACDLabs 12.01 3-[(3Z)-4-hydroxy-6-oxo-3-(2-phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]-L-alanine
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-3-[(3Z)-4-oxidanyl-6-oxidanylidene-3-(phenylhydrazinylidene)cyclohexa-1,4-dien-1-yl]propanoic acid

Formula

C15 H15 N3 O4

Formal charge

0

Molecular weight

301.297 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2C=C(O)\C(=N/Nc1ccccc1)C=C2CC(C(=O)O)N
SMILES CACTVS 3.370 N[CH](CC1=CC(=NNc2ccccc2)C(=CC1=O)O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)NN=C2C=C(C(=O)C=C2O)CC(C(=O)O)N
Canonical SMILES CACTVS 3.370 N[C@@H](CC1=C/C(=N/Nc2ccccc2)C(=CC1=O)O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)N/N=C\2/C=C(C(=O)C=C2O)C[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C15H15N3O4/c16-11(15(21)22)6-9-7-12(14(20)8-13(9)19)18-17-10-4-2-1-3-5-10/h1-5,7-8,11,17,20H,6,16H2,(H,21,22)/b18-12-/t11-/m0/s1

IUPAC InChI key

HWMLKSHHDSRXER-YXQUIRMVSA-N
YPZ

wwPDB Information

Atom count

37 (22 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

TYR

Defined at

2013-04-12

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



YPZ : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C5' C C5' N Y N 0 -5.167 -2.322 0.056
2 C4' C C4' N Y N 0 -6.361 -1.638 -0.081
3 C3' C C3' N Y N 0 -6.367 -0.256 -0.143
4 C2' C C2' N Y N 0 -5.18 0.445 -0.068
5 C1' C C1' N Y N 0 -3.978 -0.239 0.071
6 C6' C C6' N Y N 0 -3.976 -1.628 0.133
7 OX1 O OX1 N N N 0 2.968 2.466 0.063
8 NX1 N NX1 N N N 0 -2.777 0.465 0.147
9 NX2 N NX2 N N N 0 -1.663 -0.172 0.276
10 N N N N N N 0 2.96 -1.739 -1.047
11 CA C CA S N N 0 3.815 -0.708 -0.444
12 C C C N N N 0 5.16 -1.302 -0.114
13 O O O N N N 0 5.283 -2.499 -0.0090
14 CB C CB N N N 0 3.16 -0.187 0.836
15 CG C CG N N N 0 1.872 0.515 0.491
16 CD1 C CD1 N N N 0 1.899 1.873 0.109
17 CD2 C CD2 N N N 0 0.704 -0.166 0.547
18 CE1 C CE1 N N N 0 0.715 2.552 -0.217
19 CE2 C CE2 N N N 0 -0.512 0.488 0.225
20 CZ C CZ N N N 0 -0.483 1.899 -0.167
21 OH O OH N N N 0 -1.631 2.548 -0.48
22 OXT O OXT N N Y 0 6.222 -0.5 0.063
23 H5' H H5' N N N 0 -5.167 -3.401 0.108
24 H4' H H4' N N N 0 -7.291 -2.183 -0.141
25 H3' H H3' N N N 0 -7.301 0.275 -0.251
26 H2' H H2' N N N 0 -5.185 1.524 -0.117
27 H6' H H6' N N N 0 -3.044 -2.164 0.24
28 H1 H H1 N N N 0 -2.78 1.434 0.104
29 H H H N N N 0 2.826 -2.513 -0.414
30 H2 H H2 N N Y 0 2.075 -1.351 -1.337
31 HA H HA N N N 0 3.943 0.114 -1.148
32 HB2 H HB2 N N N 0 2.95 -1.023 1.503
33 HB3 H HB3 N N N 0 3.834 0.512 1.331
34 HD2 H HD2 N N N 0 0.698 -1.206 0.837
35 HE1 H HE1 N N N 0 0.751 3.592 -0.508
36 HH H HH N N N 0 -1.505 3.475 -0.725
37 HXT H HXT N N Y 0 7.064 -0.927 0.273



YPZ : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5' C4' C C doub 1.3828453 N Y
2 C5' C6' C C sing 1.3805963 N Y
3 C4' C3' C C sing 1.3834031 N Y
4 C6' C1' C C doub 1.3903844 N Y
5 C3' C2' C C doub 1.3805778 N Y
6 C1' C2' C C sing 1.3899572 N Y
7 C1' NX1 C N sing 1.3941997 N N
8 NX1 NX2 N N sing 1.289731 N N
9 OH CZ O C sing 1.355387 N N
10 N CA N C sing 1.4688754 N N
11 NX2 CE2 N C doub 1.3277808 Z N
12 CZ CE2 C C sing 1.4647273 N N
13 CZ CE1 C C doub 1.3653252 N N
14 CE2 CD2 C C sing 1.4177644 N N
15 CE1 CD1 C C sing 1.4032723 N N
16 CD2 CG C C doub 1.3531892 N N
17 CD1 CG C C sing 1.4109632 N N
18 CD1 OX1 C O doub 1.2233258 N N
19 CA CB C C sing 1.5293351 N N
20 CA C C C sing 1.5069045 N N
21 CG CB C C sing 1.5069084 N N
22 C O C O doub 1.2078754 N N
23 C OXT C O sing 1.3425263 N N
24 C5' H5' C H sing 1.0802523 N N
25 C4' H4' C H sing 1.0795949 N N
26 C3' H3' C H sing 1.079806 N N
27 C2' H2' C H sing 1.0801237 N N
28 C6' H6' C H sing 1.0804485 N N
29 NX1 H1 N H sing 0.96995825 N N
30 N H N H sing 1.0088216 N N
31 N H2 N H sing 1.0088949 N N
32 CA HA C H sing 1.0898092 N N
33 CB HB2 C H sing 1.0899013 N N
34 CB HB3 C H sing 1.0899092 N N
35 CD2 HD2 C H sing 1.0796926 N N
36 CE1 HE1 C H sing 1.0805448 N N
37 OH HH O H sing 0.9670729 N N
38 OXT HXT O H sing 0.9671572 N N



YPZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YPZ 2e2t Open in New Window Polymer component 1 1