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 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
Ligand General Information  Top
Ligand Name lipid X Ligand Info
Canonical SMILES CCCCCCCCCCCC(CC(=O)NC1C(C(C(OC1OP(=O)(O)O)CO)O)OC(=O)CC(CCCCCCCCCCC)O)O
InChI 1S/C34H66NO12P/c1-3-5-7-9-11-13-15-17-19-21-26(37)23-29(39)35-31-33(32(41)28(25-36)45-34(31)47-48(42,43)44)46-30(40)24-27(38)22-20-18-16-14-12-10-8-6-4-2/h26-28,31-34,36-38,41H,3-25H2,1-2H3,(H,35,39)(H2,42,43,44)/t26-,27-,28-,31-,32-,33-,34-/m1/s1
InChIKey HEHQDWUWJVPREQ-XQJZMFRCSA-N
PubChem Compound ID 123907
Drug Binding Sites of Target  Top
PDB ID: 2E59      Crystal structure of human MD-2 in complex with lipid IVa
Method X-ray diffraction Resolution 2.21 Å Mutation No [1]
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)
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
PDB ID: 4G8A      Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS
Method X-ray diffraction Resolution 2.40 Å Mutation Yes [2]
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
4.797
ILE52
3.884
LEU54
3.878
ILE80
3.908
VAL82
3.278
LEU87
3.438
ARG90
3.410
SER120
4.480
PHE121
3.270
Residue
Distance (Å)
LYS122
2.949
GLY123
4.559
ILE124
3.461
PHE126
3.606
TYR131
4.062
CYS133
4.281
VAL135
4.206
PHE151
3.615
ILE153
4.760
References  Top
REF 1 Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa. Science. 2007 Jun 15;316(5831):1632-4.
REF 2 Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. J Biol Chem. 2012 Nov 23;287(48):40611-7.

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