Binding Site Information of Target

Content Navigation (  All   None )                                      
Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T71907 Target Info
Target Name Survival motor neuron protein (SMN1)
Synonyms SMNT; SMNC; SMN2; SMN; Gemin-1; Component of gems 1
Target Type Successful Target
Gene Name SMN1
UniProt ID
SMN_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: N,N-dimethylarginine Ligand Info
Structure Description Solution structure of SMN Tudor domain in complex with asymmetrically dimethylated arginine PDB:4A4G
Method Solution NMR Resolution N.A. Mutation No [1]
PDB Sequence
NTAASLQQWK
93
VGDKCSAIWS
103
EDGCIYPATI
113
ASIDFKRETC
123
VVVYTGYGNR
133

EEQNLSDLLS
143
PICE
Residue
Distance (Å)
TRP102
2.337
GLU104
4.818
TYR109
2.525
PRO110
4.287
Residue
Distance (Å)
TYR127
2.321
TYR130
2.395
GLY131
4.799
ASN132
1.682
Ligand Name: SDMA Ligand Info
Structure Description Solution structure of SMN Tudor domain in complex with symmetrically dimethylated arginine PDB:4A4E
Method Solution NMR Resolution N.A. Mutation No [1]
PDB Sequence
NTAASLQQWK
93
VGDKCSAIWS
103
EDGCIYPATI
113
ASIDFKRETC
123
VVVYTGYGNR
133

EEQNLSDLLS
143
PICE
Residue
Distance (Å)
TRP102
1.877
GLU104
4.901
ASP105
1.653
TYR109
2.285
PRO110
4.581
Residue
Distance (Å)
TYR127
2.195
TYR130
2.330
GLY131
4.368
ASN132
2.027
Ligand Name: 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine Ligand Info
Structure Description Crystal Structure of tudor domain of SMN1 in complex with a small organic molecule PDB:4QQ6
Method X-ray diffraction Resolution 1.75 Å Mutation No [2]
PDB Sequence
QQWKVGDKCS
99
AIWSEDGCIY
109
PATIASIDFK
119
RETCVVVYTG
129
YGNREEQNLS
139

DLLSPICE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .36X or .36X2 or .36X3 or :336X;style chemicals stick;color identity;select .A:102 or .A:105 or .A:109 or .A:127 or .A:130 or .A:132; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP102
3.349
ASP105
4.836
TYR109
3.160
Residue
Distance (Å)
TYR127
3.501
TYR130
3.229
ASN132
3.012
Ligand Name: 4-(4-fluorobenzyl)-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine Ligand Info
Structure Description Tudor domain of SMN in complex with a small molecule PDB:7W2P
Method X-ray diffraction Resolution 1.15 Å Mutation No [2]
PDB Sequence
NTAASLQQWK
93
VGDKCSAIWS
103
EDGCIYPATI
113
ASIDFKRETC
123
VVVYTGYGNR
133

EEQNLSDLLS
143
PICE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8AI or .8AI2 or .8AI3 or :38AI;style chemicals stick;color identity;select .A:102 or .A:105 or .A:107 or .A:109 or .A:127 or .A:130 or .A:132; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP102
3.359
ASP105
3.482
CYS107
4.287
TYR109
3.532
Residue
Distance (Å)
TYR127
3.478
TYR130
3.246
ASN132
2.979
Ligand Name: 1,2-dimethylquinolin-4-imine Ligand Info
Structure Description Tudor domain of SMN in complex with a small molecule PDB:7W30
Method X-ray diffraction Resolution 1.80 Å Mutation No [2]
PDB Sequence
SLQQWKVGDK
97
CSAIWSEDGC
107
IYPATIASID
117
FKRETCVVVY
127
TGYGNREEQN
137

LSDLLSPICE
147
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8AT or .8AT2 or .8AT3 or :38AT;style chemicals stick;color identity;select .A:90 or .A:102 or .A:105 or .A:109 or .A:127 or .A:130 or .A:132 or .A:143; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN90
3.445
TRP102
3.279
ASP105
4.165
TYR109
3.210
Residue
Distance (Å)
TYR127
3.384
TYR130
3.294
ASN132
3.000
SER143
3.325
References  Top
REF 1 Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins. Nat Struct Mol Biol. 2011 Nov 20;18(12):1414-20.
REF 2 A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II. Nat Commun. 2022 Sep 16;13(1):5453.

If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.