Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T61698 Target Info
Target Name Interleukin-2 (IL2)
Synonyms TCGF; T-cell growth factor; IL-2; Aldesleukin
Target Type Successful Target
Gene Name IL2
Biochemical Class Cytokine: interleukin
UniProt ID
IL2_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: SP2456 Ligand Info
Structure Description Low Micromolar Small Molecule Inhibitor of IL-2 PDB:1PW6
Method X-ray diffraction Resolution 2.60 Å Mutation No [1]
PDB Sequence
STKKTQLQLE
15
HLLLDLQMIL
25
NGINNYKNPK
35
LTRMLTFKFY
45
MPKKATELKH
55

LQCLEEELKP
65
LEEVLNLAQR
81
PRDLISNINV
91
IVLELKGSET
101
TFMCEYADET
111

ATIVEFLNRW
121
ITFCQSIIST
131
L
Residue
Distance (Å)
LYS35
4.061
ARG38
3.452
MET39
3.405
THR41
3.619
PHE42
3.296
LYS43
2.809
PHE44
4.032
Residue
Distance (Å)
TYR45
3.376
GLU62
2.985
PRO65
3.392
VAL69
3.245
LEU72
3.336
ALA73
3.611
THR111
3.931
Ligand Name: SP4160 Ligand Info
Structure Description Structure of SP4160 Bound to IL-2 V69A PDB:1QVN
Method X-ray diffraction Resolution 2.70 Å Mutation Yes [2]
PDB Sequence
SSSTKKTQLQ
13
LEHLLLDLQM
23
ILNGINNYKN
33
PKLTRMLTFK
43
FYMPKKATEL
53

KHLQCLEEEL
63
KPLEEALNLA
73
QRPRDLISNI
89
NVIVLELKGS
99
ETTFMCEYAD
109

ETATIVEFLN
119
RWITFCQSII
129
STL
Residue
Distance (Å)
PRO34
2.796
LYS35
2.868
ARG38
2.998
MET39
3.222
THR41
3.510
PHE42
3.574
LYS43
3.416
PHE44
4.232
Residue
Distance (Å)
TYR45
3.326
GLU62
3.216
PRO65
3.998
GLU68
4.853
ALA69
3.749
LEU72
3.442
ALA73
3.641
THR111
4.999
Ligand Name: 2-[3-Methyl-4-(N-methyl-guanidino)-butyrylamino]-3-(4-phenylethynyl-phenyl)-propionic acid methyl ester Ligand Info
Structure Description Crystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Aminoiminomethyl)-3-piperidinyl]-1-oxoethyl]-4-(phenylethynyl)-L-phenylalanine methyl ester PDB:1M48
Method X-ray diffraction Resolution 1.95 Å Mutation No [3]
PDB Sequence
SSSTKKTQLQ
13
LEHLLLDLQM
23
ILNGINNYKN
33
PKLTRMLTFK
43
FYMPKKATEL
53

KHLQCLEEEL
63
KPLEEVLNLA
73
QRPRDLISNI
89
NVIVLELKGS
99
ETTFMCEYAD
109

ETATIVEFLN
119
RWITFCQSII
129
STL
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FRG or .FRG2 or .FRG3 or :3FRG;style chemicals stick;color identity;select .A:35 or .A:38 or .A:39 or .A:41 or .A:42 or .A:43 or .A:44 or .A:45 or .A:62 or .A:65 or .A:69 or .A:72 or .A:73; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS35
3.350
ARG38
3.438
MET39
3.611
THR41
3.398
PHE42
3.576
LYS43
2.643
PHE44
3.656
Residue
Distance (Å)
TYR45
3.154
GLU62
2.748
PRO65
3.686
VAL69
4.187
LEU72
3.507
ALA73
3.191
Ligand Name: 2-[2-(1-Carbamimidoyl-piperidin-3-YL)-acetylamino]-3-{4-[2-(3-oxalyl-1H-indol-7-YL)ethyl]-phenyl}-propionic acid methyl ester Ligand Info
Structure Description Crystal Structure of Human Interleukin-2 Complexed with SP-1985 PDB:1M49
Method X-ray diffraction Resolution 2.00 Å Mutation No [3]
PDB Sequence
SSSTKKTQLQ
13
LEHLLLDLQM
23
ILNGINNYKN
33
PKLTRMLTFK
43
FYMPKKATEL
53

KHLQCLEEEL
63
KPLEEVLNLA
73
QRPRDLISNI
89
NVIVLELKGS
99
ETTFMCEYAD
109

ETATIVEFLN
119
RWITFCQSII
129
STL
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CMM or .CMM2 or .CMM3 or :3CMM;style chemicals stick;color identity;select .A:34 or .A:35 or .A:38 or .A:39 or .A:41 or .A:42 or .A:43 or .A:44 or .A:45 or .A:62 or .A:65 or .A:69 or .A:72 or .A:73; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PRO34
4.043
LYS35
3.525
ARG38
3.270
MET39
3.676
THR41
3.471
PHE42
3.639
LYS43
2.801
Residue
Distance (Å)
PHE44
3.735
TYR45
3.227
GLU62
2.833
PRO65
3.507
VAL69
4.082
LEU72
3.731
ALA73
3.280
Ligand Name: 2-[2-(2-Cyclohexyl-2-guanidino-acetylamino)-acetylamino]-N-(3-mercapto-propyl)-propionamide Ligand Info
Structure Description Crystal Structure of Human Interleukin-2 K43C Covalently Modified at C43 with 2-[2-(2-Cyclohexyl-2-guanidino-acetylamino)-acetylamino]-N-(3-mercapto-propyl)-propionamide PDB:1M4B
Method X-ray diffraction Resolution 2.15 Å Mutation Yes [3]
PDB Sequence
SSTKKTQLQL
14
EHLLLDLQMI
24
LNGINNYKNP
34
KLTRMLTFCF
44
YMPKKATELK
54

HLQCLEEELK
64
PLEEVLNLAR
83
DLISNINVIV
93
LELKGFMCEY
107
ADETATIVEF
117

LNRWITFCQS
127
IISTLT
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Residue
Distance (Å)
THR41
3.963
PHE42
3.291
CYS43
2.038
PHE44
3.809
TYR45
3.362
Residue
Distance (Å)
GLU61
4.778
GLU62
2.749
PRO65
3.646
GLU68
4.472
Ligand Name: (1H-Indol-3-YL)-(2-mercapto-ethoxyimino)-acetic acid Ligand Info
Structure Description Crystal Structure of Human Interleukin-2 Y31C Covalently Modified at C31 with (1H-Indol-3-yl)-(2-mercapto-ethoxyimino)-acetic acid PDB:1M4A
Method X-ray diffraction Resolution 2.18 Å Mutation Yes [3]
PDB Sequence
TKKTQLQLEH
16
LLLDLQMILN
26
GINNCKNPKL
36
TRMLTFKFYM
46
PKKATELKHL
56

QCLEEELKPL
66
EEVLNLALRP
82
RDLISNINVI
92
VLELFMCEYA
108
DETATIVEFL
118

NRWITFCQSI
128
ISTL
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Residue
Distance (Å)
GLY27
4.807
ILE28
4.007
CYS31
2.010
LYS32
4.942
LYS35
3.358
LEU36
3.590
Residue
Distance (Å)
ARG38
4.528
MET39
3.520
PHE42
3.552
VAL69
3.790
LEU72
3.420
ALA73
3.108
Ligand Name: 3-Mercapto-1-(1,3,4,9-tetrahydro-B-carbolin-2-YL)-propan-1-one Ligand Info
Structure Description Crystal Structure Of Human Interleukin-2 Y31C Covalently Modified At C31 With 3-Mercapto-1-(1,3,4,9-tetrahydro-B-carbolin-2-yl)-propan-1-one PDB:1NBP
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [4]
PDB Sequence
STKKTQLQLE
15
HLLLDLQMIL
25
NGINNCKNPK
35
LTRMLTFKFY
45
MPKKATELKH
55

LQCLEEELKP
65
LEEVLNLAQF
78
HLRPRDLISN
88
INVIVLELKG
98
FMCEYADETA
112

TIVEFLNRWI
122
TFCQSIISTL
132
T
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Residue
Distance (Å)
MET23
4.465
ILE24
4.054
GLY27
3.568
ILE28
4.121
ASN30
4.732
CYS31
2.036
LYS32
4.971
LYS35
3.769
MET39
4.152
Residue
Distance (Å)
LEU70
3.598
ALA73
3.657
GLN74
3.202
PHE78
3.325
LEU80
3.775
ARG81
4.068
PRO82
3.597
LEU85
3.510
Ligand Name: 5-[2,3-Dichloro-4-(5-{1-[2-(2-guanidino-4-methyl-pentanoylamino)-acetyl]-piperidin-4-YL}-1-methyl-1H-pyrazol-3-YL)-phenoxymethyl]-furan-2-carboxylic acid Ligand Info
Structure Description Structure of a 60 nM Small Molecule Bound to a Hot Spot on IL-2 PDB:1PY2
Method X-ray diffraction Resolution 2.80 Å Mutation No [1]
PDB Sequence
STKKTQLQLE
15
HLLLDLQMIL
25
NGINNYPKLT
37
RMLTFKFYMP
47
KKATELKHLQ
57

CLEEELKPLE
67
EVLNLAFRPR
83
DLISNINVIV
93
LELKETTFMC
105
EYADETATIV
115

EFLNRWITFC
125
QSIISTL
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Residue
Distance (Å)
PRO34
3.140
LYS35
3.871
ARG38
3.109
MET39
3.640
THR41
3.491
PHE42
3.300
LYS43
2.941
PHE44
3.634
Residue
Distance (Å)
TYR45
3.407
GLU62
2.813
PRO65
3.645
VAL69
3.806
LEU72
3.423
ALA73
3.819
THR111
3.785
Ligand Name: 5-Methylfuran-2-carboxylic acid Ligand Info
Structure Description Small molecular fragment bound to crystal contact interface of Interleukin-2 PDB:4NEJ
Method X-ray diffraction Resolution 1.92 Å Mutation No [5]
PDB Sequence
SSSTKKTQLQ
13
LEHLLLDLQM
23
ILNGINNYKN
33
PKLTRMLTFK
43
FYMPKKATEL
53

KHLQCLEEEL
63
KPLEEVLNLA
73
QSDLISNINV
91
IVLELKGFMC
105
EYADETATIV
115

EFLNRWITFS
125
QSIISTLT
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Residue
Distance (Å)
GLN11
3.853
LEU12
4.044
GLU15
2.743
THR41
3.685
PHE42
3.359
Residue
Distance (Å)
LYS43
2.882
PHE44
3.430
GLU62
4.950
PRO65
3.885
VAL69
4.547
Ligand Name: 5-[(2,3-Dichlorophenoxy)methyl]furan-2-carboxylic acid Ligand Info
Structure Description Small molecular fragment bound to crystal contact interface of Interleukin-2 PDB:4NEM
Method X-ray diffraction Resolution 1.93 Å Mutation No [6]
PDB Sequence
STKKTQLQLE
15
HLLLDLQMIL
25
NGINNYKNPK
35
LTRMLTFKFY
45
MPKKATELKH
55

LQCLEEELKP
65
LEEVLNLAQD
84
LISNINVIVL
94
ELKFMCEYAD
109
ETATIVEFLN
119

RWITFSQSII
129
STLT
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .2JY or .2JY2 or .2JY3 or :32JY;style chemicals stick;color identity;select .A:9 or .A:12 or .A:13 or .A:16 or .A:88 or .A:91 or .A:92 or .A:95; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS9
4.028
LEU12
3.361
GLN13
3.196
HIS16
3.260
Residue
Distance (Å)
ASN88
2.874
VAL91
3.865
ILE92
3.521
GLU95
4.540
References  Top
REF 1 Potent small-molecule binding to a dynamic hot spot on IL-2. J Am Chem Soc. 2003 Dec 17;125(50):15280-1.
REF 2 Hot-spot mimicry of a cytokine receptor by a small molecule. Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15422-7.
REF 3 Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1603-8.
REF 4 Discovery and characterization of cooperative ligand binding in the adaptive region of interleukin-2. Biochemistry. 2003 Jun 3;42(21):6475-83.
REF 5 Small molecular fragments bound to binding energy hot-spot in crystal contact interface of Interleukin-2
REF 6 Small molecular fragments bound to binding energy hot-spot in crystal contact interface of Interleukin-2

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