Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T82254 Target Info
Target Name Apoptosis regulator BAK (BAK)
Synonyms CDN1; Bcl2like protein 7; Bcl2L7; Bcl2-L-7; Bcl2 homologous antagonist/killer; Bcl-2-like protein 7; Bcl-2 homologous antagonist/killer
Target Type Literature-reported Target
Gene Name BAK1
Biochemical Class B-cell lymphoma Bcl-2
UniProt ID
BAK_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: (Hydroxyethyloxy)Tri(Ethyloxy)Octane Ligand Info
Structure Description Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4 PDB:6UXQ
Method X-ray diffraction Resolution 1.70 Å Mutation No [1]
PDB Sequence
GPLGSSTMGQ
73
VGRQLAIIGD
83
DINRRYDSEF
93
QTMLQHLQPT
103
AENAYEYFTK
113

IATSLFESGI
123
NWGRVVALLG
133
FGYRLALHVY
143
QHGL
Residue
Distance (Å)
PHE111
4.797
GLU120
2.931
SER121
3.633
LEU132
3.910
GLY135
3.698
Residue
Distance (Å)
TYR136
3.706
ALA139
3.526
LEU140
3.661
TYR143
3.769
Ligand Name: (S)-2-Aminooctanedioic acid Ligand Info
Structure Description Bak in complex with Bim-h3Pc PDB:5VWZ
Method X-ray diffraction Resolution 1.62 Å Mutation Yes [2]
PDB Sequence
SMSEEQVAQD
30
TEEVFRSYVF
40
YRHQQEQEAE
50
GVAAPADPEM
60
VTLPLQPSST
70

MGQVGRQLAI
80
IGDDINRRYD
90
SEFQTMLQHL
100
QPTAENAYEY
110
FTKIATSLFE
120

SGINWGRVVA
130
LLGFGYRLAL
140
HVYQHGLTGF
150
LGQVTRFVVD
160
FMLHHSIARW
170

IAQRGGWVAA
180
LNLGNG
Residue
Distance (Å)
TYR38
4.030
ARG42
2.819
ILE85
4.216
ASN86
3.416
TYR89
3.455
PHE93
4.064
Residue
Distance (Å)
VAL129
4.882
ALA130
4.143
GLY133
3.319
PHE134
4.525
ARG137
2.554
Ligand Name: Trifluoroacetic Acid Ligand Info
Structure Description Bak core latch dimer in complex with Bim-BH3 - Cubic PDB:5VWV
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [2]
PDB Sequence
GPLGSMSEEQ
26
VAQDTEEVFR
36
SYVFYRHQQE
46
QEAEGVAAPA
56
DPEMVTLPLQ
66

PSSTMGQVGR
76
QLAIIGDDIN
86
RRYDSEFQTM
96
LQHLQPTAEN
106
AYEYFTKIAT
116

SLFESGINWG
126
RVVALLGFGY
136
RLALHVYQHG
146
LTGFLGQVTR
156
FVVDFMLHHS
166

IARWIAQRGG
176
WVAALNLGNG
186
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TFA or .TFA2 or .TFA3 or :3TFA;style chemicals stick;color identity;select .A:38 or .A:42 or .A:86 or .A:89 or .A:93 or .A:129 or .A:130 or .A:133 or .A:134 or .A:137; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR38
3.740
ARG42
2.780
ASN86
2.979
TYR89
3.954
PHE93
3.607
Residue
Distance (Å)
VAL129
4.920
ALA130
3.781
GLY133
3.392
PHE134
4.048
ARG137
2.664
Ligand Name: 1,2-Dioctanoyl-sn-glycero-3-phosphoserine Ligand Info
Structure Description Crystal structure of BAK core domain BH3-groove-dimer in complex with phosphatidylserine PDB:6UXN
Method X-ray diffraction Resolution 2.49 Å Mutation No [1]
PDB Sequence
GSSTMGQVGR
76
QLAIIGDDIN
86
RRYDSEFQTM
96
LQHLQPTAEN
106
AYEYFTKIAT
116

SLFESGINWG
126
RVVALLGFGY
136
RLALHVYQHG
146
LT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8SP or .8SP2 or .8SP3 or :38SP;style chemicals stick;color identity;select .A:95 or .A:99 or .A:123 or .A:124 or .A:125 or .A:128 or .A:129 or .A:132; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR95
3.249
HIS99
2.540
ILE123
3.271
ASN124
3.522
Residue
Distance (Å)
TRP125
3.308
VAL128
3.840
VAL129
3.996
LEU132
3.669
Ligand Name: 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine Ligand Info
Structure Description Crystal structure of BAK core domain BH3-groove-dimer in complex with E. coli lipid PDB:6UXM
Method X-ray diffraction Resolution 2.49 Å Mutation No [1]
PDB Sequence
GSSTMGQVGR
76
QLAIIGDDIN
86
RRYDSEFQTM
96
LQHLQPTAEN
106
AYEYFTKIAT
116

SLFESGINWG
126
RVVALLGFGY
136
RLALHVYQH
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PEE or .PEE2 or .PEE3 or :3PEE;style chemicals stick;color identity;select .A:86 or .A:135 or .A:136 or .A:137 or .A:139 or .A:140; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ASN86
3.523
GLY135
4.545
TYR136
2.657
Residue
Distance (Å)
ARG137
3.589
ALA139
4.322
LEU140
4.856
Ligand Name: 3,3'-[(E)-Diazenediyl]bis[6-(2-chloroacetamido)benzene-1-sulfonic acid] Ligand Info
Structure Description SOLUTION STRUCTURE OF AN APOPTOSIS ACTIVATING PHOTOSWITCHABLE BAK PEPTIDE BOUND to BCL-XL PDB:2LP8
Method Solution NMR Resolution N.A. Mutation Yes [3]
PDB Sequence
GCVGRALAAF
1011
GDCINR
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .33B or .33B2 or .33B3 or :333B;style chemicals stick;color identity;select .B:1002 or .B:1003 or .B:1004 or .B:1006 or .B:1007 or .B:1010 or .B:1011 or .B:1013 or .B:1014 or .B:1017; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY1002
4.073
CYS1003
1.808
VAL1004
3.459
ARG1006
2.005
ALA1007
2.224
Residue
Distance (Å)
ALA1010
1.807
PHE1011
1.701
ASP1013
2.947
CYS1014
1.808
ARG1017
3.350
References  Top
REF 1 BAK core dimers bind lipids and can be bridged by them. Nat Struct Mol Biol. 2020 Nov;27(11):1024-1031.
REF 2 Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design. Mol Cell. 2017 Nov 16;68(4):659-672.e9.
REF 3 NMR solution structure of a photoswitchable apoptosis activating Bak peptide bound to Bcl-xL. J Am Chem Soc. 2012 May 9;134(18):7644-7.

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