Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T64410 Target Info
Target Name Bacterial DD-carboxypeptidase (Bact vanYB)
Synonyms vanYB; DD-peptidase; DD-carboxypeptidase; D-alanyl-D-alanine carboxypeptidase-transpeptidase
Target Type Successful Target
Gene Name Bact vanYB
Biochemical Class Peptidase
UniProt ID
VANY_ENTFA
Ligand General Information  Top
Ligand Name D-Alanine Ligand Info
Canonical SMILES CC(C(=O)O)N
InChI 1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
InChIKey QNAYBMKLOCPYGJ-UWTATZPHSA-N
PubChem Compound ID 71080
Drug Binding Sites of Target  Top
PDB ID: 5ZHW      VanYB in complex with D-Alanine-D-Alanine
Method X-ray diffraction Resolution 2.18 Å Mutation No [1]
PDB Sequence
EWSLILVNRQ
97
NPIPAQYDVE
107
LEQLSNGERI
117
DIRISPYLQD
127
LFDAARADGV
137

YPIVASGYRT
147
TEKQQEIDEK
158
VAEYKAKGYT
168
SAQAKAEAET
178
WVAVPGTSEH
188

QLGLAVDINA
198
DGIHSTGNEV
208
YRWLDENSYR
218
FGFIRRYPPD
228
KTEITGVSNE
238

PWHYRYVGIE
248
AATKIYHQGL
258
CLEEYLNTEK
268
Residue
Distance (Å)
ARG146
3.494
GLN151
3.029
ILE154
3.943
TRP179
3.052
VAL180
3.751
ALA181
3.091
SER186
2.538
GLU187
3.868
Residue
Distance (Å)
HIS188
3.434
ASP195
3.141
TYR225
3.826
VAL235
4.114
GLU238
3.265
TRP240
3.575
HIS241
3.146
PDB ID: 6A6A      VanYB in complex with D-Alanine
Method X-ray diffraction Resolution 2.26 Å Mutation No [1]
PDB Sequence
EWSLILVNRQ
97
NPIPAQYDVE
107
LEQLSNGERI
117
DIRISPYLQD
127
LFDAARADGV
137

YPIVASGYRT
147
TEKQQEIMDE
157
KVAEYKAKGY
167
TSAQAKAEAE
177
TWVAVPGTSE
187

HQLGLAVDIN
197
ADGIHSTGNE
207
VYRWLDENSY
217
RFGFIRRYPP
227
DKTEITGVSN
237

EPWHYRYVGI
247
EAATKIYHQG
257
LCLEEYLNTE
267
KLE
Residue
Distance (Å)
ARG146
3.447
GLN151
2.945
TRP179
2.742
VAL180
3.556
ALA181
3.125
SER186
2.479
Residue
Distance (Å)
GLU187
4.208
HIS188
3.266
TYR225
3.293
VAL235
4.211
GLU238
3.267
HIS241
3.871
References  Top
REF 1 Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanY(B). Int J Biol Macromol. 2018 Nov;119:335-344.

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