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 2-Deoxy-3-O-[(3r)-3-Hydroxytetradecanoyl]-2-{[(3r)-3-Hydroxytetradecanoyl]amino}-4-O-Phosphono-Beta-D-Glucopyranose Ligand Info
Canonical SMILES CCCCCCCCCCCC(CC(=O)NC1C(C(C(OC1O)CO)OP(=O)(O)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(47-48(42,43)44)28(25-36)45-34(31)41)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 AJRPJFBMHCTNGK-XQJZMFRCSA-N
PubChem Compound ID 16214777
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)
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
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)
ILE46
4.377
VAL48
4.051
ILE52
4.352
LEU61
4.062
ILE63
3.402
TYR65
3.582
LEU71
4.054
LEU74
4.194
PHE76
3.848
ILE94
4.632
TYR102
3.347
Residue
Distance (Å)
PHE104
3.876
VAL113
4.615
ILE117
3.636
SER118
2.689
PHE119
3.295
SER120
2.783
PHE121
4.007
LEU146
4.783
PHE147
4.376
PHE151
3.842
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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