Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T58080 Target Info
Target Name Beta-2-microglobulin (B2M)
Synonyms Beta-2-microglobulin
Target Type Literature-reported Target
Gene Name B2M
UniProt ID
B2MG_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Urea Ligand Info
Structure Description Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3 PDB:1XR9
Method X-ray diffraction Resolution 1.79 Å Mutation No [1]
PDB Sequence
IQRTPKIQVY
10
SRHPAENGKS
20
NFLNCYVSGF
30
HPSDIEVDLL
40
KNGERIEKVE
50

HSDLSFSKDW
60
SFYLLYYTEF
70
TPTEKDEYAC
80
RVNHVTLSQP
90
KIVKWDRDM
Residue
Distance (Å)
TYR10
3.908
SER11
2.871
ARG12
4.075
HIS13
3.573
Residue
Distance (Å)
PRO14
3.576
ARG97
4.436
MET99
4.425
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: Beta-D-Glucose Ligand Info
Structure Description Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22 PDB:6V7Z
Method X-ray diffraction Resolution 2.75 Å Mutation No [2]
PDB Sequence
MIQRTPKIQV
9
YSRHPAENGK
19
SNFLNCYVSG
29
FHPSDIEVDL
39
LKNGERIEKV
49

EHSDLSFSKD
59
WSFYLLYYTE
69
FTPTEKDEYA
79
CRVNHVTLSQ
89
PKIVKWDRD
Residue
Distance (Å)
GLU50
4.588
HIS51
3.195
SER52
3.791
Residue
Distance (Å)
ASP53
3.560
LEU65
4.620
TYR67
2.193
Ligand Name: 2-(2-{2-[2-(2-Methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol Ligand Info
Structure Description CRYSTAL STRUCTURE OF HLA-A*0201/MAGE-A4-PEPTIDE COMPLEX PDB:1I4F
Method X-ray diffraction Resolution 1.40 Å Mutation No [3]
PDB Sequence
MIQRTPKIQV
9
YSRHPAENGK
19
SNFLNCYVSG
29
FHPSDIEVDL
39
LKNGERIEKV
49

EHSDLSFSKD
59
WSFYLLYYTE
69
FTPTEKDEYA
79
CRVNHVTLSQ
89
PKIVKWDRDM
99
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1PG or .1PG2 or .1PG3 or :31PG;style chemicals stick;color identity;select .B:56 or .B:57 or .B:58 or .B:60; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE56
3.853
SER57
3.371
Residue
Distance (Å)
LYS58
2.800
TRP60
3.671
Ligand Name: 2-[4-(Dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium Ligand Info
Structure Description Protein induced photophysical changes to the amyloid indicator dye, thioflavin T PDB:3MYZ
Method X-ray diffraction Resolution 1.60 Å Mutation Yes [4]
PDB Sequence
MIQRTPKIQV
9
YSRFPAENGK
19
SNFLNCYVSG
29
FHPSDIEVDL
39
LKNGERIEKV
49

EHSDLSFSKD
59
SFYLLYYTEF
70
TPTEKDEYAC
80
RVNHVTLSQP
90
KIVKWDR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TFX or .TFX2 or .TFX3 or :3TFX;style chemicals stick;color identity;select .A:8 or .A:10 or .A:26 or .A:28 or .A:42 or .A:43 or .A:63 or .A:73 or .A:75 or .A:76 or .A:77; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN8
3.288
TYR10
3.385
TYR26
3.506
SER28
3.323
ASN42
3.182
GLY43
3.988
Residue
Distance (Å)
TYR63
4.603
THR73
4.802
LYS75
3.434
ASP76
3.827
GLU77
3.185
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: 1-[7-(3-Fluorophenyl)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]ethanone Ligand Info
Structure Description Crystal structure of FcRn bound to UCB-84 PDB:6C98
Method X-ray diffraction Resolution 1.85 Å Mutation No [5]
PDB Sequence
IQRTPKIQVY
10
SRHPAENGKS
20
NFLNCYVSGF
30
HPSDIEVDLL
40
KNGERIEKVE
50

HSDLSFSKDW
60
SFYLLYYTEF
70
TPTEKDEYAC
80
RVNHVTLSQP
90
KIVKWDRDM
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ER7 or .ER72 or .ER73 or :3ER7;style chemicals stick;color identity;select .B:26 or .B:51 or .B:52 or .B:53 or .B:55 or .B:63 or .B:64 or .B:65 or .B:67; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.544
HIS51
4.981
SER52
3.118
ASP53
3.400
SER55
4.385
Residue
Distance (Å)
TYR63
3.370
LEU64
3.431
LEU65
3.273
TYR67
4.171
Ligand Name: Methyl 7-(3,5-difluorophenyl)-5-pyridin-3-yl-[1,2,4]triazolo[1,5-a]pyrimidine-6-carboxylate Ligand Info
Structure Description Crystal structure of FcRn bound to UCB-303 PDB:6C99
Method X-ray diffraction Resolution 2.00 Å Mutation No [5]
PDB Sequence
IQRTPKIQVY
10
SRHPAENGKS
20
NFLNCYVSGF
30
HPSDIEVDLL
40
KNGERIEKVE
50

HSDLSFSKDW
60
SFYLLYYTEF
70
TPTEKDEYAC
80
RVNHVTLSQP
90
KIVKWDRDM
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EQY or .EQY2 or .EQY3 or :3EQY;style chemicals stick;color identity;select .B:26 or .B:51 or .B:52 or .B:53 or .B:55 or .B:63 or .B:64 or .B:65 or .B:67; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR26
3.702
HIS51
4.550
SER52
3.055
ASP53
3.298
SER55
3.732
Residue
Distance (Å)
TYR63
3.411
LEU64
3.571
LEU65
3.266
TYR67
3.321
Ligand Name: 5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxamide Ligand Info
Structure Description Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand PDB:7AFV
Method X-ray diffraction Resolution 2.40 Å Mutation Yes [6]
PDB Sequence
MIQVYSRHPA
15
ENGKSNFLNC
25
YVSGFHPSDI
35
EVDLLKNGER
45
IEKVEHCDLS
55

FSKDWSFYLL
65
YYTEFTPTEK
75
DEYACRVNHV
85
TLSQPKIVKW
95
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SJK or .SJK2 or .SJK3 or :3SJK;style chemicals stick;color identity;select .A:6 or .A:8 or .A:10 or .A:26 or .A:52 or .A:63 or .A:65; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET6
4.211
GLN8
4.982
TYR10
3.582
TYR26
3.298
Residue
Distance (Å)
CYS52
2.165
TYR63
4.811
LEU65
4.267
References  Top
REF 1 Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype. Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1300-10.
REF 2 A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.. doi:10.1038/s43018-020-00111-6.
REF 3 High-resolution structure of HLA-A*0201 in complex with a tumour-specific antigenic peptide encoded by the MAGE-A4 gene. J Mol Biol. 2001 Jul 27;310(5):1167-76.
REF 4 Protein-induced photophysical changes to the amyloid indicator dye thioflavin T. Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16863-8.
REF 5 Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR. PLoS Biol. 2018 May 21;16(5):e2006192.
REF 6 Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules. J Am Chem Soc. 2020 Dec 9;142(49):20845-20854.

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