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BCL2_HUMAN_2_207

Apoptosis regulator Bcl-2 [Bcl-2 family]

Composition of the binding site

Protein chains monomer
A1 (BCL2_HUMAN):99, 100, 103, 104, 107, 108, 110:112, 114, 115, 118, 119, 129, 132, 133, 135:140, 143:146, 148, 149, 152, 153, 156, 198, 201:20799, 100, 103, 104, 107, 108, 110:112, 114, 115, 118, 119, 129, 132, 133, 135:140, 143:146, 148, 149, 152, 153, 156, 198, 201:207

Full PDB list

2w3l, 2xa0, 4aq3, 4ieh, 4lvt, 4lxd, 4man, 5agw, 5agx, 5jsn (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
9
9
A
1
0
0
D
1
0
3
F
1
0
4
R
1
0
7
Y
1
0
8
R
1
1
0
D
1
1
1
F
1
1
2
M
1
1
5
Q
1
1
8
L
1
1
9
R
1
2
9
T
1
3
2
V
1
3
3
E
1
3
6
L
1
3
7
R
1
3
9
D
1
4
0
N
1
4
3
W
1
4
4
G
1
4
5
R
1
4
6
V
1
4
8
A
1
4
9
E
1
5
2
F
1
5
3
V
1
5
6
F
1
9
8
L
2
0
1
Y
2
0
2
G
2
0
3
S
2
0
5
[1]4ieh.a 1e959 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4lvt.a 1xj65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4lxd.a 1xv48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4man.a 1y165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[2]2w3l.a dro42 E . . . . . . . . . G . . . . . . . . . . . . . . . . . . . . . .
[2]2xa0.a LSECLRRIGDELDSNM126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]4aq3.b 398,398106 . . . . . . G . . . . . . . . . . . . . . . . . . . . . . . . . -
[3]4aq3.c 39853 . . . . . . G . . . . . . . . . . . . . . . . . . . . . . . . . -
[4]5jsn.a D-AASLQANGDIFYAIL118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[5]5agx.a aceIxcpIAQajeLRmh8IGDmh8FNxcpYY166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
Q
9
9
A
1
0
0
D
1
0
3
F
1
0
4
R
1
0
7
Y
1
0
8
R
1
1
0
D
1
1
1
F
1
1
2
E
1
1
4
M
1
1
5
Q
1
1
8
L
1
1
9
R
1
2
9
T
1
3
2
V
1
3
3
E
1
3
5
E
1
3
6
L
1
3
7
F
1
3
8
R
1
3
9
D
1
4
0
N
1
4
3
W
1
4
4
G
1
4
5
R
1
4
6
V
1
4
8
A
1
4
9
E
1
5
2
F
1
5
3
V
1
5
6
F
1
9
8
L
2
0
1
Y
2
0
2
G
2
0
3
P
2
0
4
S
2
0
5
M
2
0
6
R
2
0
7
[1]4ieh.a . . . . * * . * . . * . . . . . . * . . . . . . . . . . . . . . . * * * - - -
[1]4lvt.a . . . . . * * * . . * . . . . . . * . . . . . . . . . . . . . . . * * . - - -
[1]4lxd.a . . . . * * . * . . * . . . . . . * . . . . . . . * . . . . . . . * . . - - -
[1]4man.a . . . . . * . * . . * . . . . . . * . . . . . . . . . . . . . . . * . . - - -
[2]2w3l.a E . . . * * . . * . . G . . . . . * . . . . . . . . . . . . . . . * * . * * -
[2]2xa0.a . . . . . * . . * . * . . . . . . . . . * . . . . * . . . . . . . * . . * * -
[3]4aq3.b . . . . . * G * * . * . . . . . . . . . . . . . . . . . . . . . . * . - - - -
[3]4aq3.c . . . . * * G * * . * . . . . . . . . . . . . . . . . . . . . . . * . - - - -
[4]5jsn.a . . . . . * . . * . * . . . . . . . . . . . . . . . . . . . . . . * * * * * *
[5]5agx.a . . . . . * . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . - - -

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4ieh.a:1e9
4lvt.a:1xj
4lxd.a:1xv
4man.a:1y1
2w3l.a:dro
2xa0.a:LSECLRRIGDELDSNM
4aq3.b:398
4aq3.c:398
5jsn.a:D-AASLQANGDIFYAIL
5agx.a:aceIxcpIAQajeLRmh8IGDmh8FNxcpYY
[1] 4ieh.a
0
3.3 0.1 0.4 3.1 12 4.8 1.5 5.4 9.6
[1] 4lvt.a 0.8
0
0.2 4.2 4.7 8.0 6.6 4.0 3.4 8.4
[1] 4lxd.a 0.3 3.4
0
0 4.6 14 4.5 2.7 5.5 9.7
[1] 4man.a 0.5 3.3 0.1
0
4.4 9.5 4.3 2.5 4.8 8.2
[2] 2w3l.a 5.3 8.6 4.0 5.3
0
8.5 11 3.2 3.2 5.9
[2] 2xa0.a 4.0 4.7 1.0 4.4 3.4
0.3
9.7 1.5 1.6 5.7
[3] 4aq3.b 2.9 2.4 2.7 5.5 0.6 6.0
0
0 1.5 7.1
[3] 4aq3.c 2.6 2.3 2.2 5.4 0.7 6.3 0.1
0
1.9 7.1
[4] 5jsn.a 5.1 8.3 3.2 7.2 2.2 6.1 12 0.6
0.1
5.7
[5] 5agx.a 2.4 4.7 3.1 3.0 3.7 5.5 6.6 5.3 2.0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (5 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4ieh.a
4lvt.a
4lxd.a
4man.a
2w3l.a
2xa0.a
4aq3.b
4aq3.c
5jsn.a
5agx.a
[1] 4ieh.a
0
.24 .20 .16 .35 .45 .25 .24 .55 .42
[1] 4lvt.a .24
0
.20 .14 .38 .49 .26 .27 .52 .41
[1] 4lxd.a .20 .20
0
.18 .42 .52 .29 .29 .61 .48
[1] 4man.a .16 .14 .18
0
.39 .46 .23 .24 .54 .38
[2] 2w3l.a .35 .38 .42 .39
0
.21 .35 .35 .33 .41
[2] 2xa0.a .45 .49 .52 .46 .21
0
.33 .33 .32 .39
[3] 4aq3.b .25 .26 .29 .23 .35 .33
0
.03 .42 .25
[3] 4aq3.c .24 .27 .29 .24 .35 .33 .03
0
.44 .26
[4] 5jsn.a .55 .52 .61 .54 .33 .32 .42 .44
0
.46
[5] 5agx.a .42 .41 .48 .38 .41 .39 .25 .26 .46
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4ieh.a
4lvt.a
4lxd.a
4man.a
2w3l.a
2xa0.a
4aq3.b
4aq3.c
5jsn.a
5agx.a
[1] 4ieh.a
0
0.9 0.6 0.6 1.4 2.3 1.1 1.1 1.8 1.3
[1] 4lvt.a 0.9
0
0.8 0.8 1.6 2.4 1.3 1.3 1.8 1.5
[1] 4lxd.a 0.6 0.8
0
0.4 1.5 2.4 0.9 0.9 1.9 1.4
[1] 4man.a 0.6 0.8 0.4
0
1.6 2.4 1.1 1.1 1.9 1.4
[2] 2w3l.a 1.4 1.6 1.5 1.6
0
1.9 1.0 0.9 1.1 1.5
[2] 2xa0.a 2.3 2.4 2.4 2.4 1.9
0
2.3 2.2 2.4 1.9
[3] 4aq3.b 1.1 1.3 0.9 1.1 1.0 2.3
0
0.2 1.4 1.3
[3] 4aq3.c 1.1 1.3 0.9 1.1 0.9 2.2 0.2
0
1.5 1.2
[4] 5jsn.a 1.8 1.8 1.9 1.9 1.1 2.4 1.4 1.5
0
1.9
[5] 5agx.a 1.3 1.5 1.4 1.4 1.5 1.9 1.3 1.2 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4ieh.a
4lvt.a
4lxd.a
4man.a
2w3l.a
2xa0.a
4aq3.b
4aq3.c
5jsn.a
5agx.a
[1] 4ieh.a
0
1.7 1.3 1.3 1.9 3.6 1.8 1.8 2.6 2.2
[1] 4lvt.a 1.7
0
1.8 1.5 2.3 3.7 1.8 1.8 2.5 2.4
[1] 4lxd.a 1.3 1.8
0
1.3 1.9 3.8 1.8 1.7 2.7 2.3
[1] 4man.a 1.3 1.5 1.3
0
2.2 3.7 1.8 1.7 2.7 2.2
[2] 2w3l.a 1.9 2.3 1.9 2.2
0
3.2 1.6 1.6 2.1 2.3
[2] 2xa0.a 3.6 3.7 3.8 3.7 3.2
0
3.0 3.0 3.4 2.8
[3] 4aq3.b 1.8 1.8 1.8 1.8 1.6 3.0
0
0.6 1.7 1.9
[3] 4aq3.c 1.8 1.8 1.7 1.7 1.6 3.0 0.6
0
1.7 1.9
[4] 5jsn.a 2.6 2.5 2.7 2.7 2.1 3.4 1.7 1.7
0
2.3
[5] 5agx.a 2.2 2.4 2.3 2.2 2.3 2.8 1.9 1.9 2.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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