Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T52382 Target Info
Target Name Lymphocyte antigen 96 (LY96)
Synonyms MD-2 protein; MD-2; LY96; ESOP-1
Target Type Literature-reported Target
Gene Name LY96
UniProt ID
LY96_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: ERITORAN Ligand Info
Structure Description Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex PDB:2Z65
Method X-ray diffraction Resolution 2.70 Å Mutation No [1]
PDB Sequence
QKQYWVCNSS
28
DASISYTYCD
38
KMQYPISINV
48
NPCIELKGSK
58
GLLHIFYIPR
68

RDLKQLYFNL
78
YITVNTMNLP
88
KRKEVICRGS
98
DDDYSFCRAL
108
KGETVNTTIS
118

FSFKGIKFSK
128
GKYKCVVEAI
138
SGSPEEMLFC
148
LEFVILHQPN
158
Residue
Distance (Å)
ILE32
4.452
ILE46
3.506
VAL48
4.481
ILE52
4.217
LEU54
4.852
LEU61
3.964
ILE63
3.727
TYR65
3.497
LEU71
4.181
LEU74
4.596
PHE76
3.934
LEU78
4.528
ILE80
4.211
LEU87
3.649
ILE94
4.934
TYR102
3.372
PHE104
3.522
Residue
Distance (Å)
VAL113
4.771
ILE117
3.773
SER118
3.776
PHE119
3.335
SER120
2.924
PHE121
3.251
LYS122
4.072
GLY123
3.468
ILE124
4.136
TYR131
4.190
CYS133
3.873
VAL135
4.395
LEU146
4.839
PHE147
4.006
LEU149
4.478
PHE151
3.471
ILE153
4.475
Ligand Name: Myristic acid Ligand Info
Structure Description Crystal structure of human MD-2 PDB:2E56
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
EAQKQYWVCN
26
SSDASISYTY
36
CDKMQYPISI
46
NVNPCIELKG
56
SKGLLHIFYI
66

PRRDLKQLYF
76
NLYITVNTMN
86
LPKRKEVICR
96
GSDDDYSFCR
106
ALKGETVNTT
116

ISFSFKGIKF
126
SKGKYKCVVE
136
AISGSPEEML
146
FCLEFVILHQ
156
PNSN
Residue
Distance (Å)
ILE32
4.276
ILE44
4.638
ILE46
4.340
VAL48
3.569
ILE52
3.151
LEU61
3.752
ILE63
4.142
TYR65
4.270
LEU71
4.406
LEU74
4.064
PHE76
4.051
LEU78
4.272
GLU92
3.930
VAL93
4.556
ILE94
4.019
Residue
Distance (Å)
TYR102
4.064
PHE104
3.798
VAL113
4.942
ILE117
4.181
SER118
3.549
PHE119
3.612
SER120
2.843
PHE121
3.939
CYS133
3.816
VAL135
4.268
PHE147
4.273
LEU149
4.483
PHE151
3.892
ILE153
4.387
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Lauric acid Ligand Info
Structure Description Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS PDB:4G8A
Method X-ray diffraction Resolution 2.40 Å Mutation Yes [3]
PDB Sequence
QKQYWVCNSS
28
DASISYTYCD
38
KMQYPISINV
48
NPCIELKGSK
58
GLLHIFYIPR
68

RDLKQLYFNL
78
YITVNTMNLP
88
KRKEVICRGS
98
DDDYSFCRAL
108
KGETVNTTIS
118

FSFKGIKFSK
128
GKYKCVVEAI
138
SGSPEEMLFC
148
LEFVILHQPN
158
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DAO or .DAO2 or .DAO3 or :3DAO;style chemicals stick;color identity;select .C:54 or .C:78 or .C:80 or .C:90 or .C:92 or .C:126 or .C:131 or .C:133 or .C:153; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU54
3.901
LEU78
3.572
ILE80
3.856
ARG90
3.672
GLU92
3.806
Residue
Distance (Å)
PHE126
3.873
TYR131
3.595
CYS133
4.136
ILE153
3.930
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: 2-Deoxy-3-O-[(3r)-3-Hydroxytetradecanoyl]-2-{[(3r)-3-Hydroxytetradecanoyl]amino}-4-O-Phosphono-Beta-D-Glucopyranose Ligand Info
Structure Description Crystal structure of human MD-2 in complex with lipid IVa PDB:2E59
Method X-ray diffraction Resolution 2.21 Å Mutation No [2]
PDB Sequence
EAQKQYWVCN
26
SSDASISYTY
36
CDKMQYPISI
46
NVNPCIELKG
56
SKGLLHIFYI
66

PRRDLKQLYF
76
NLYITVNTMN
86
LPKRKEVICR
96
GSDDDYSFCR
106
ALKGETVNTT
116

ISFSFKGIKF
126
SKGKYKCVVE
136
AISGSPEEML
146
FCLEFVILHQ
156
PNSN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LP4 or .LP42 or .LP43 or :3LP4;style chemicals stick;color identity;select .A:32 or .A:48 or .A:52 or .A:54 or .A:61 or .A:78 or .A:80 or .A:90 or .A:119 or .A:120 or .A:121 or .A:122 or .A:123 or .A:124 or .A:131 or .A:132 or .A:133 or .A:151 or .A:153; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE32
4.702
VAL48
4.362
ILE52
2.808
LEU54
4.225
LEU61
4.533
LEU78
4.307
ILE80
3.950
ARG90
3.331
PHE119
4.033
SER120
2.663
Residue
Distance (Å)
PHE121
3.360
LYS122
3.052
GLY123
4.544
ILE124
3.483
TYR131
4.096
LYS132
4.939
CYS133
3.827
PHE151
3.915
ILE153
3.840
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: lipid X Ligand Info
Structure Description Crystal structure of human MD-2 in complex with lipid IVa PDB:2E59
Method X-ray diffraction Resolution 2.21 Å Mutation No [2]
PDB Sequence
EAQKQYWVCN
26
SSDASISYTY
36
CDKMQYPISI
46
NVNPCIELKG
56
SKGLLHIFYI
66

PRRDLKQLYF
76
NLYITVNTMN
86
LPKRKEVICR
96
GSDDDYSFCR
106
ALKGETVNTT
116

ISFSFKGIKF
126
SKGKYKCVVE
136
AISGSPEEML
146
FCLEFVILHQ
156
PNSN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LP5 or .LP52 or .LP53 or :3LP5;style chemicals stick;color identity;select .A:44 or .A:46 or .A:61 or .A:63 or .A:65 or .A:71 or .A:74 or .A:76 or .A:78 or .A:92 or .A:94 or .A:102 or .A:104 or .A:117 or .A:118 or .A:119 or .A:120 or .A:122 or .A:133 or .A:135 or .A:146 or .A:147 or .A:149 or .A:151; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE44
4.611
ILE46
3.839
LEU61
3.855
ILE63
3.703
TYR65
3.979
LEU71
4.204
LEU74
3.522
PHE76
3.696
LEU78
3.998
GLU92
3.733
ILE94
4.103
TYR102
3.895
Residue
Distance (Å)
PHE104
3.826
ILE117
3.961
SER118
3.585
PHE119
3.385
SER120
2.873
LYS122
3.790
CYS133
4.942
VAL135
4.020
LEU146
4.840
PHE147
4.206
LEU149
4.633
PHE151
4.121
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: 3-Hydroxytetradecanoic acid Ligand Info
Structure Description Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex PDB:3FXI
Method X-ray diffraction Resolution 3.10 Å Mutation No [4]
PDB Sequence
QKQYWVCNSS
28
DASISYTYCD
38
KMQYPISINV
48
NPCIELKGSK
58
GLLHIFYIPR
68

RDLKQLYFNL
78
YITVNTMNLP
88
KRKEVICRGS
98
DDDYSFCRAL
108
KGETVNTTIS
118

FSFKGIKFSK
128
GKYKCVVEAI
138
SGSPEEMLFC
148
LEFVILHQPN
158
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FTT or .FTT2 or .FTT3 or :3FTT;style chemicals stick;color identity;select .C:24 or .C:32 or .C:46 or .C:48 or .C:52 or .C:54 or .C:61 or .C:63 or .C:65 or .C:71 or .C:74 or .C:76 or .C:80 or .C:82 or .C:87 or .C:90 or .C:94 or .C:102 or .C:104 or .C:117 or .C:118 or .C:119 or .C:120 or .C:121 or .C:122 or .C:123 or .C:124 or .C:125 or .C:126 or .C:127 or .C:131 or .C:133 or .C:135 or .C:146 or .C:147 or .C:151 or .C:153; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
VAL24
3.712
ILE32
3.890
ILE46
4.044
VAL48
3.789
ILE52
4.166
LEU54
4.973
LEU61
3.914
ILE63
3.802
TYR65
3.556
LEU71
3.453
LEU74
3.844
PHE76
3.829
ILE80
4.626
VAL82
3.622
LEU87
3.681
ARG90
3.975
ILE94
4.411
TYR102
3.920
PHE104
3.633
Residue
Distance (Å)
ILE117
3.549
SER118
3.644
PHE119
3.546
SER120
3.762
PHE121
3.532
LYS122
2.935
GLY123
4.367
ILE124
3.524
LYS125
4.733
PHE126
3.839
SER127
3.696
TYR131
3.333
CYS133
3.734
VAL135
4.543
LEU146
4.361
PHE147
4.187
PHE151
3.480
ILE153
4.658
References  Top
REF 1 Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. Cell. 2007 Sep 7;130(5):906-17.
REF 2 Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa. Science. 2007 Jun 15;316(5831):1632-4.
REF 3 Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. J Biol Chem. 2012 Nov 23;287(48):40611-7.
REF 4 The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Nature. 2009 Apr 30;458(7242):1191-5.

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