Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T51499 Target Info
Target Name Ganglioside GM2 activator (GM2A)
Synonyms Sphingolipid activator protein 3; SAP3; Ganglioside GM2 activator isoform short; GM2AP; GM2A; Cerebroside sulfate activator protein
Target Type Clinical trial Target
Gene Name GM2A
UniProt ID
SAP3_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Oleic acid Ligand Info
Structure Description Crystal Structure Analysis of GM2-activator protein complexed with phosphatidylcholine PDB:2AG4
Method X-ray diffraction Resolution 1.80 Å Mutation No [1]
PDB Sequence
HMSSFSWDNC
10
DEGKDPAVIR
20
SLTLEPDPIV
30
VPGNVTLSVV
40
GSTSVPLSSP
50

LKVDLVLEKE
60
VAGLWIKIPC
70
TDYIGSCTFE
80
HFCDVLDMLI
90
PTGEPCPEPL
100

RTYGLPCHCP
110
FKEGTYSLPK
120
SEFVVPDLEL
130
PSWLTTGNYR
140
IESVLSSSGK
150

RLGCIKIAAS
160
LKGI
Residue
Distance (Å)
LEU37
3.295
VAL39
3.760
PRO97
3.831
GLU98
3.722
Residue
Distance (Å)
PRO99
4.264
LEU100
4.067
LEU118
4.004
PHE123
4.120
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Lauric acid Ligand Info
Structure Description Crystal Structure analysis of GM2-Activator protein complexed with phosphatidylcholine PDB:2AF9
Method X-ray diffraction Resolution 2.00 Å Mutation No [1]
PDB Sequence
MSSFSWDNCD
9
EGKDPAVIRS
19
LTLEPDPIVV
29
PGNVTLSVVG
39
STSVPLSSPL
49

KVDLVLEKEV
59
AGLWIKIPCT
69
DYIGSCTFEH
79
FCDVLDMLIP
89
TGEPCPEPLR
99

TYGLPCHCPF
109
KEGTYSLPKS
119
EFVVPDLELP
129
SWLTTGNYRI
139
ESVLSSSGKR
149

LGCIKIAASL
159
KGI
Residue
Distance (Å)
LEU45
3.872
LEU49
3.870
VAL51
3.461
LEU53
3.965
LEU55
4.279
LYS57
3.511
ILE66
4.456
PHE80
3.186
PHE109
3.072
LEU132
3.035
THR133
4.533
TYR137
3.146
Residue
Distance (Å)
ARG138
4.151
ILE139
3.326
GLU140
4.535
SER141
3.314
LEU143
4.991
ILE153
3.348
LYS154
4.842
ILE155
3.328
ALA156
3.948
ALA157
3.513
LEU159
3.568
Ligand Name: Lpc-Ether Ligand Info
Structure Description Human GM2 Activator Protein PAF complex PDB:1TJJ
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
HMSSFSWDNC
10
DEGKDPAVIR
20
SLTLEPDPIV
30
VPGNVTLSVV
40
GSTSVPLSSP
50

LKVDLVLEKE
60
VAGLWIKIPC
70
TDYIGSCTFE
80
HFCDVLDMLI
90
PTGEPCPEPL
100

RTYGLPCHCP
110
FKEGTYSLPK
120
SEFVVPDLEL
130
PSWLTTGNYR
140
IESVLSSSGK
150

RLGCIKIAAS
160
LKGI
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LPE or .LPE2 or .LPE3 or :3LPE;style chemicals stick;color identity;select .A:17 or .A:18 or .A:19 or .A:41 or .A:42 or .A:43 or .A:47 or .A:53 or .A:55 or .A:73 or .A:79 or .A:82 or .A:85 or .A:86 or .A:89 or .A:90 or .A:100 or .A:106 or .A:107 or .A:111 or .A:116 or .A:143 or .A:144 or .A:145 or .A:153 or .A:154 or .A:155; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA17
3.696
VAL18
3.435
ILE19
3.743
GLY41
3.939
SER42
3.952
THR43
4.239
LEU47
4.126
VAL53
3.431
LEU55
3.762
TYR73
4.641
PHE79
3.984
PHE82
3.566
VAL85
4.580
LEU86
3.718
Residue
Distance (Å)
LEU89
3.596
ILE90
3.731
LEU100
4.321
PRO106
3.095
CYS107
4.401
PHE111
3.795
TYR116
3.493
SER143
2.936
VAL144
4.342
LEU145
3.915
GLY153
3.749
CYS154
3.594
ILE155
3.249
Ligand Name: Myristic acid Ligand Info
Structure Description Crystal Structure analysis of GM2-Activator protein complexed with phosphatidylcholine PDB:2AF9
Method X-ray diffraction Resolution 2.00 Å Mutation No [1]
PDB Sequence
MSSFSWDNCD
9
EGKDPAVIRS
19
LTLEPDPIVV
29
PGNVTLSVVG
39
STSVPLSSPL
49

KVDLVLEKEV
59
AGLWIKIPCT
69
DYIGSCTFEH
79
FCDVLDMLIP
89
TGEPCPEPLR
99

TYGLPCHCPF
109
KEGTYSLPKS
119
EFVVPDLELP
129
SWLTTGNYRI
139
ESVLSSSGKR
149

LGCIKIAASL
159
KGI
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MYR or .MYR2 or .MYR3 or :3MYR;style chemicals stick;color identity;select .A:22 or .A:27 or .A:29 or .A:33 or .A:35 or .A:121 or .A:123 or .A:124 or .A:125 or .A:126 or .A:128 or .A:133 or .A:159; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU22
4.190
ILE27
3.411
VAL29
3.868
VAL33
3.451
LEU35
4.580
PHE121
3.710
VAL123
3.943
Residue
Distance (Å)
PRO124
4.466
ASP125
4.487
LEU126
3.090
LEU128
3.420
THR133
3.664
LEU159
3.823
Ligand Name: PAF Ligand Info
Structure Description Human GM2 Activator Protein PAF complex PDB:1TJJ
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
HMSSFSWDNC
10
DEGKDPAVIR
20
SLTLEPDPIV
30
VPGNVTLSVV
40
GSTSVPLSSP
50

LKVDLVLEKE
60
VAGLWIKIPC
70
TDYIGSCTFE
80
HFCDVLDMLI
90
PTGEPCPEPL
100

RTYGLPCHCP
110
FKEGTYSLPK
120
SEFVVPDLEL
130
PSWLTTGNYR
140
IESVLSSSGK
150

RLGCIKIAAS
160
LKGI
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PFS or .PFS2 or .PFS3 or :3PFS;style chemicals stick;color identity;select .A:19 or .A:22 or .A:24 or .A:29 or .A:37 or .A:39 or .A:40 or .A:41 or .A:57 or .A:68 or .A:74 or .A:105 or .A:116 or .A:117 or .A:118 or .A:128 or .A:130 or .A:139 or .A:140 or .A:141 or .A:155 or .A:157 or .A:158 or .A:159 or .A:161; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ILE19
3.596
LEU22
4.124
LEU24
3.577
ILE29
4.926
LEU37
4.070
VAL39
3.231
VAL40
4.580
GLY41
4.252
LEU57
2.904
ILE68
3.594
ILE74
4.473
LEU105
4.122
TYR116
3.271
Residue
Distance (Å)
SER117
3.644
LEU118
3.396
LEU128
4.300
LEU130
3.844
TYR139
3.048
ARG140
3.217
ILE141
3.089
ILE155
4.127
ILE157
3.141
ALA158
3.605
ALA159
3.188
LEU161
2.904
Ligand Name: 1-Stearoyl-sn-glycero-3-phosphocholine Ligand Info
Structure Description Crystal Structure Analysis of GM2-activator protein complexed with phosphatidylcholine PDB:2AG4
Method X-ray diffraction Resolution 1.80 Å Mutation No [1]
PDB Sequence
HMSSFSWDNC
10
DEGKDPAVIR
20
SLTLEPDPIV
30
VPGNVTLSVV
40
GSTSVPLSSP
50

LKVDLVLEKE
60
VAGLWIKIPC
70
TDYIGSCTFE
80
HFCDVLDMLI
90
PTGEPCPEPL
100

RTYGLPCHCP
110
FKEGTYSLPK
120
SEFVVPDLEL
130
PSWLTTGNYR
140
IESVLSSSGK
150

RLGCIKIAAS
160
LKGI
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LP3 or .LP32 or .LP33 or :3LP3;style chemicals stick;color identity;select .A:17 or .A:18 or .A:19 or .A:41 or .A:42 or .A:43 or .A:47 or .A:82 or .A:86 or .A:89 or .A:90 or .A:95 or .A:96 or .A:97 or .A:100 or .A:101 or .A:105 or .A:106 or .A:107 or .A:111 or .A:114 or .A:116 or .A:143 or .A:145 or .A:152 or .A:153 or .A:154 or .A:155; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA17
3.025
VAL18
4.222
ILE19
3.855
GLY41
2.890
SER42
2.978
THR43
3.379
LEU47
3.333
PHE82
3.798
LEU86
3.883
LEU89
3.929
ILE90
4.309
PRO95
4.321
CYS96
4.780
PRO97
3.494
Residue
Distance (Å)
LEU100
3.847
ARG101
4.909
LEU105
4.654
PRO106
2.924
CYS107
4.337
PHE111
3.609
GLY114
4.896
TYR116
3.224
SER143
4.799
LEU145
3.576
LEU152
4.997
GLY153
3.734
CYS154
4.475
ILE155
3.325
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Distearoyl phosphatidic acid Ligand Info
Structure Description GM2-activator Protein crystal structure PDB:1PUB
Method X-ray diffraction Resolution 2.51 Å Mutation No [3]
PDB Sequence
SSFSWDNCDE
10
GKDPAVIRSL
20
TLEPDPIIVP
30
GNVTLSVMGS
40
TSVPLSSPLK
50

VDLVLEKEVA
60
GLWIKIPCTD
70
YIGSCTFEHF
80
CDVLDMLIPT
90
GEPCPEPLRT
100

YGLPCHCPFK
110
EGTYSLPKSE
120
FVVPDLELPS
130
WLTTGNYRIE
140
SVLSSSGKRL
150

GCIKIAASLK
160
GI
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3PH or .3PH2 or .3PH3 or :33PH;style chemicals stick;color identity;select .A:15 or .A:16 or .A:17 or .A:20 or .A:22 or .A:27 or .A:35 or .A:37 or .A:39 or .A:40 or .A:41 or .A:45 or .A:51 or .A:53 or .A:55 or .A:66 or .A:72 or .A:98 or .A:103 or .A:104 or .A:109 or .A:114 or .A:137 or .A:139 or .A:141 or .A:143 or .A:151 or .A:152 or .A:153 or .A:155 or .A:157 or .A:159; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA15
3.918
VAL16
4.083
ILE17
3.921
LEU20
3.851
LEU22
3.900
ILE27
3.530
LEU35
4.886
VAL37
3.430
GLY39
4.839
SER40
3.754
THR41
4.731
LEU45
4.914
VAL51
4.579
LEU53
4.037
LEU55
4.028
ILE66
4.887
Residue
Distance (Å)
ILE72
4.814
LEU98
4.996
LEU103
4.566
PRO104
3.826
PHE109
4.573
TYR114
4.660
TYR137
4.314
ILE139
4.600
SER141
3.693
LEU143
4.045
GLY151
4.403
CYS152
4.769
ILE153
3.667
ILE155
3.616
ALA157
4.868
LEU159
3.384
References  Top
REF 1 Crystal structure analysis of phosphatidylcholine-GM2-activator product complexes: evidence for hydrolase activity. Biochemistry. 2005 Oct 18;44(41):13510-21.
REF 2 Evidence for lipid packaging in the crystal structure of the GM2-activator complex with platelet activating factor. J Mol Biol. 2004 Sep 10;342(2):585-92.
REF 3 Structural analysis of lipid complexes of GM2-activator protein. J Mol Biol. 2003 Aug 22;331(4):951-64.

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