Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T58093 Target Info
Target Name Staphylococcus Peptide deformylase (Stap-coc def)
Synonyms def; Stap-coc Polypeptide deformylase
Target Type Clinical trial Target
Gene Name Stap-coc def
Biochemical Class Carbon-nitrogen hydrolase
UniProt ID
DEF_STAAU
Drug Binding Sites of Target  Top
Ligand Name: 3-Sulfinoalanine Ligand Info
Structure Description Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin PDB:1Q1Y
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [1]
PDB Sequence
MLTMKDIIRD
10
GHPTLRQKAA
20
ELELPLTKEE
30
KETLIAMREF
40
LVNSQDEEIA
50

KRYGLRSGVG
60
LAAPQINISK
70
RMIAVLIPDD
80
GSGKSYDYML
90
VNPKIVSHSV
100

QEAYLPTGEG
110
LSVDDNVAGL
121
VHRHNRITIK
131
AKDIEGNDIQ
141
LRLKGYPAIV
151

FQHEIDHLNG
161
VMFYDHIDKD
171
HPLQPHTDAV
181
EVLEH
Residue
Distance (Å)
ARG56
2.804
GLN65
2.924
GLU109
4.510
GLY110
1.328
LEU112
1.330
SER113
2.667
Residue
Distance (Å)
VAL114
2.918
ASP115
4.803
HIS154
3.754
HIS158
3.223
MET163
3.038
PHE164
3.545
Ligand Name: Actinonin Ligand Info
Structure Description Crystal Structures of Peptide Deformylase from Staphylococcus aureus Complexed with Actinonin PDB:1Q1Y
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [1]
PDB Sequence
MLTMKDIIRD
10
GHPTLRQKAA
20
ELELPLTKEE
30
KETLIAMREF
40
LVNSQDEEIA
50

KRYGLRSGVG
60
LAAPQINISK
70
RMIAVLIPDD
80
GSGKSYDYML
90
VNPKIVSHSV
100

QEAYLPTGEG
110
LSVDDNVAGL
121
VHRHNRITIK
131
AKDIEGNDIQ
141
LRLKGYPAIV
151

FQHEIDHLNG
161
VMFYDHIDKD
171
HPLQPHTDAV
181
EVLEH
Residue
Distance (Å)
ARG56
3.404
SER57
3.323
GLY58
3.223
VAL59
2.797
GLY60
3.131
LEU61
4.368
ALA62
4.655
GLN65
2.725
LEU105
3.517
GLU109
3.411
Residue
Distance (Å)
GLY110
3.590
LEU112
2.702
SER113
4.559
TYR147
4.425
ILE150
3.665
VAL151
3.663
HIS154
3.363
GLU155
2.688
HIS158
2.924
GLU185
3.691
Ligand Name: L-[(N-Hydroxyamino)carbonyl]phenylalanine Ligand Info
Structure Description K4U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus PDB:6JFS
Method X-ray diffraction Resolution 2.25 Å Mutation No [2]
PDB Sequence
MLTMKDIIRD
10
GHPTLRQKAA
20
ELELPLTKEE
30
KETLIAMREF
40
LVNSQDEEIA
50

KRYGLRSGVG
60
LAAPQINISK
70
RMIAVLIPDD
80
GSGKSYDYML
90
VNPKIVSHSV
100

QEAYLPTGEG
110
CLSVDDNVAG
120
LVHRHNRITI
130
KAKDIEGNDI
140
QLRLKGYPAI
150

VFQHEIDHLN
160
GVMFYDHIDK
170
NHPLQPHTDA
180
VEV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LHY or .LHY2 or .LHY3 or :3LHY;style chemicals stick;color identity;select .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:65 or .A:105 or .A:108 or .A:109 or .A:110 or .A:111 or .A:112 or .A:113 or .A:147 or .A:150 or .A:151 or .A:154 or .A:155 or .A:158; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER57
3.930
GLY58
2.897
VAL59
2.787
GLY60
2.905
LEU61
4.315
GLN65
2.781
LEU105
3.476
GLY108
4.564
GLU109
3.430
GLY110
3.628
Residue
Distance (Å)
CYS111
3.172
LEU112
2.999
SER113
4.975
TYR147
4.849
ILE150
4.476
VAL151
4.666
HIS154
3.310
GLU155
2.679
HIS158
2.914
Ligand Name: S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate Ligand Info
Structure Description K3U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus PDB:6JFR
Method X-ray diffraction Resolution 2.40 Å Mutation No [3]
PDB Sequence
MLTMKDIIRD
10
GHPTLRQKAA
20
ELELPLTKEE
30
KETLIAMREF
40
LVNSQDEEIA
50

KRYGLRSGVG
60
LAAPQINISK
70
RMIAVLIPDD
80
GSGKSYDYML
90
VNPKIVSHSV
100

QEAYLPTGEG
110
CLSVDDNVAG
120
LVHRHNRITI
130
KAKDIEGNDI
140
QLRLKGYPAI
150

VFQHEIDHLN
160
GVMFYDHIDK
170
NHPLQPHTDA
180
VEV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K3U or .K3U2 or .K3U3 or :3K3U;style chemicals stick;color identity;select .A:45 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:65 or .A:105 or .A:108 or .A:109 or .A:110 or .A:111 or .A:112 or .A:113 or .A:147 or .A:150 or .A:151 or .A:154 or .A:155 or .A:158; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN45
4.383
SER57
3.087
GLY58
3.451
VAL59
2.597
GLY60
2.370
LEU61
3.952
GLN65
3.356
LEU105
3.560
GLY108
4.962
GLU109
3.672
Residue
Distance (Å)
GLY110
3.031
CYS111
3.055
LEU112
2.574
SER113
4.458
TYR147
4.596
ILE150
4.268
VAL151
4.326
HIS154
3.310
GLU155
2.031
HIS158
3.870
Ligand Name: (3R)-3-benzyl-4-oxo-4-[(2-oxo-2-phenylethyl)sulfanyl]butanoic acid Ligand Info
Structure Description K1U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus PDB:6JFG
Method X-ray diffraction Resolution 2.60 Å Mutation No [4]
PDB Sequence
MLTMKDIIRD
10
GHPTLRQKAA
20
ELELPLTKEE
30
KETLIAMREF
40
LVNSQDEEIA
50

KRYGLRSGVG
60
LAAPQINISK
70
RMIAVLIPDD
80
GSGKSYDYML
90
VNPKIVSHSV
100

QEAYLPTGEG
110
CLSVDDNVAG
120
LVHRHNRITI
130
KAKDIEGNDI
140
QLRLKGYPAI
150

VFQHEIDHLN
160
GVMFYDHIDK
170
NHPLQPHTDA
180
VEV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K1U or .K1U2 or .K1U3 or :3K1U;style chemicals stick;color identity;select .A:45 or .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:65 or .A:105 or .A:109 or .A:110 or .A:111 or .A:112 or .A:113 or .A:147 or .A:150 or .A:151 or .A:154 or .A:155 or .A:158; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN45
4.639
SER57
2.930
GLY58
3.354
VAL59
2.509
GLY60
2.988
LEU61
4.800
GLN65
3.106
LEU105
3.532
GLU109
3.905
GLY110
3.073
Residue
Distance (Å)
CYS111
3.140
LEU112
2.540
SER113
4.381
TYR147
3.816
ILE150
3.972
VAL151
4.141
HIS154
3.222
GLU155
2.806
HIS158
3.563
Ligand Name: (3R,4R)-3-benzyl-4-benzylsulfanyl-4-hydroxybutanoic acid Ligand Info
Structure Description K2U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus PDB:6JFQ
Method X-ray diffraction Resolution 2.20 Å Mutation No [5]
PDB Sequence
MLTMKDIIRD
10
GHPTLRQKAA
20
ELELPLTKEE
30
KETLIAMREF
40
LVNSQDEEIA
50

KRYGLRSGVG
60
LAAPQINISK
70
RMIAVLIPDD
80
GSGKSYDYML
90
VNPKIVSHSV
100

QEAYLPTGEG
110
CLSVDDNVAG
120
LVHRHNRITI
130
KAKDIEGNDI
140
QLRLKGYPAI
150

VFQHEIDHLN
160
GVMFYDHIDK
170
NHPLQPHTDA
180
VEV
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K2U or .K2U2 or .K2U3 or :3K2U;style chemicals stick;color identity;select .A:57 or .A:58 or .A:59 or .A:60 or .A:61 or .A:65 or .A:105 or .A:109 or .A:110 or .A:111 or .A:112 or .A:113 or .A:147 or .A:150 or .A:151 or .A:154 or .A:155 or .A:158; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER57
2.952
GLY58
3.292
VAL59
2.487
GLY60
2.859
LEU61
4.805
GLN65
3.134
LEU105
3.656
GLU109
3.612
GLY110
2.859
Residue
Distance (Å)
CYS111
3.329
LEU112
2.583
SER113
4.285
TYR147
4.116
ILE150
4.267
VAL151
4.083
HIS154
3.324
GLU155
2.895
HIS158
3.657
References  Top
REF 1 Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent. Proteins. 2004 Nov 15;57(3):639-42.
REF 2 K4U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
REF 3 K3U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
REF 4 K1U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus
REF 5 K2U bound crystal structure of class II peptide deformylase from methicillin resistant Staphylococcus aureus

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