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DCAM_HUMAN_1_332

S-adenosylmethionine decarboxylase proenzyme [Eukaryotic AdoMetDC family]

Composition of the binding site

Protein chains monomer
A1 (DCAM_HUMAN):0, 7, 11, 49, 64:69, 80:82, 85, 223:229, 243:2470, 7, 11, 49, 64:69, 80:82, 85, 223:229, 243:247

Full PDB list

1i72, 1i79, 1i7b, 1i7c, 1i7m, 1jen, 1jl0, 1msv, 3dz2, 3dz3, 3dz4, 3dz5, 3dz6, 3dz7, 3ep3, 3ep4, 3ep5, 3ep6, 3ep7, 3ep8, 3ep9, 3epa, 3epb, 3h0v, 3h0w (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
.
0
S
6
9
K
8
0
T
8
1
C
8
2
T
8
5
F
2
2
3
N
2
2
4
P
2
2
5
C
2
2
6
G
2
2
7
Y
2
2
8
S
2
2
9
H
2
4
3
I
2
4
4
T
2
4
5
P
2
4
6
E
2
4
7
[1]1i72.a mao24 pyr . . . . . . . . . . . . . . . . .
[1]1i79.a mhz25 pyr . . . . . . . . . . . . . . . . .
[1]1i7b.a smm28 pyr . . . . . . . . . . . . . . . . .
[1]1i7c.a mgb13 * . . . . . . . . . . . . . . . . .
[1]1i7m.a cg17 * . . . . . . . . . . . . . . . . .
[1]3dz2.a a8m25 * . . . . . . . . . . . . . . . . .
[1]3dz3.a smm28 pyr . . . . . A . . . . . . . . . . .
[1]3dz4.a c8m26 * . . . . . . . . . . . . . . . . .
[1]3dz5.a m8m25 pyr . . . . . . . . . . . . . . . . .
[1]3dz6.a m8e28 * . . . . . . . . . . . . . . . . .
[1]3dz7.a o8m25 * . . . . . . . . . . . . . . . . .
[1]3ep3.a pyr5 - . . . . . . . . . . . . . . . . .
[1]3ep6.a pyr-smm32 - . . . . . . . . . . . . . . . . .
[1]3epb.a none * . . . . . . . . . . . . . . . . .
[1]3h0v.a m2t21 * . . . . . . . . . . . . . . . . .
[1]3h0w.a n8m22 * . . . . . . . . . . . . . . . . .
[2]1jl0.a none - . . . . . . . . . . . . A . . . .
[2]1msv.b none - . . . . . . . . . . . . . . . . .

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
.
0
F
7
E
1
1
C
4
9
V
6
4
L
6
5
S
6
6
E
6
7
S
6
8
S
6
9
K
8
0
T
8
1
C
8
2
T
8
5
F
2
2
3
N
2
2
4
P
2
2
5
C
2
2
6
G
2
2
7
Y
2
2
8
S
2
2
9
H
2
4
3
I
2
4
4
T
2
4
5
P
2
4
6
E
2
4
7
[1]1i72.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]1i79.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]1i7b.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]1i7c.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]1i7m.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3dz2.a pyr - - - - - - - - . . . . . . . . . . . . . . . . .
[1]3dz3.a pyr - - - - - - - - * . . . . A . . . . . . . . . . .
[1]3dz4.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3dz5.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3dz6.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3dz7.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3ep3.a - - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3ep6.a - - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3epb.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3h0v.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[1]3h0w.a pyr - - - - - - - - * . . . . . . . . . . . . . . . .
[2]1jl0.a - . . . . . . * * * . . . . . . . . . . . A . . . .
[2]1msv.b - . . . . . * * 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
1i72.a:mao
1i79.a:mhz
1i7b.a:smm
1i7c.a:mgb
1i7m.a:cg
3dz2.a:a8m
3dz3.a:smm
3dz4.a:c8m
3dz5.a:m8m
3dz6.a:m8e
3dz7.a:o8m
3ep3.a:pyr
3ep6.a:pyr-smm
3epb.a is apo
3h0v.a:m2t
3h0w.a:n8m
1jl0.a is apo
1msv.b is apo
[1] 1i72.a
0.7
0.8 0.6 0.2 0.4 0.1 0.9 0 0.5 0.1 0.2 4.5 3.2 - 0 0 - -
[1] 1i79.a 0.7
0.7
0.7 0.1 0.3 0.1 0.8 0 0.5 0.1 0.1 4.4 3.6 - 0 0 - -
[1] 1i7b.a 0.9 0.9
0.7
0.3 0.5 0.5 0.7 0.3 0.6 0.5 0.5 3.9 4.1 - 0 0.1 - -
[1] 1i7c.a 1.0 1.4 1.3
0.1
0.3 0.2 1.3 0.2 0.8 0.2 0.3 4.5 4.0 - 0 0 - -
[1] 1i7m.a 1.0 1.4 1.1 0
0
0.3 1.2 0.2 0.6 0.2 0.3 4.5 3.7 - 0 0 - -
[1] 3dz2.a 1.2 1.2 1.1 0.1 0.6
0.1
1.3 0.1 0.7 0.1 0.1 4.5 3.9 - 0 0 - -
[1] 3dz3.a 0.9 0.7 0.7 0 0.3 0.3
0.7
0.1 0.4 0 0.2 4.1 3.6 - 0 0 - -
[1] 3dz4.a 1.2 1.4 1.2 0.2 0.6 0.1 1.3
0.1
0.9 0.1 0.1 5.2 3.9 - 0 0 - -
[1] 3dz5.a 0.9 1.0 0.9 0.1 0.7 0.2 0.9 0
0.8
0 0.1 3.3 3.7 - 0 0 - -
[1] 3dz6.a 1.6 1.5 1.4 0.1 0.7 0.1 1.5 0.1 0.9
0.2
0.1 4.9 3.9 - 0 0 - -
[1] 3dz7.a 1.2 1.4 1.2 0.1 0.4 0.1 1.3 0 0.9 0.1
0.1
4.6 3.9 - 0 0 - -
[1] 3ep3.a 0 0 0 0 0.2 0.2 0 0.1 0 0.2 0.2
0.7
0.5 - 0 0 - -
[1] 3ep6.a 0 0 0 0.2 0.3 0.5 0 0.3 0.1 0.5 0.5 0.9
0.7
- 0 0.1 - -
[1] 3epb.a 1.6 1.7 1.5 0.3 0.6 0.5 1.7 0.2 1.5 0.2 0.3 4.4 4.4
-
0 0 - -
[1] 3h0v.a 1.4 1.5 1.3 0.1 0.6 0.1 1.5 0.1 1.0 0.2 0.1 5.2 4.0 -
0
0 - -
[1] 3h0w.a 1.4 1.5 1.2 0.2 0.6 0.1 1.3 0.1 0.9 0.1 0.1 5.2 3.9 - 0
0
- -
[2] 1jl0.a 2.1 2.0 4.3 0.8 1.5 0.7 5.2 0.9 1.7 3.1 0.4 4.5 7.4 - 0.1 0.4
-
-
[2] 1msv.b 5.4 5.7 6.5 5.2 6.1 3.1 6.1 4.6 5.3 5.9 3.1 4.2 9.0 - 2.6 2.8 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1i72.a
1i79.a
1i7b.a
1i7c.a
1i7m.a
3dz2.a
3dz3.a
3dz4.a
3dz5.a
3dz6.a
3dz7.a
3ep3.a
3ep6.a
3epb.a
3h0v.a
3h0w.a
1jl0.a
1msv.b
[1] 1i72.a
0
.02 .03 .05 .05 .05 .03 .05 .03 .05 .04 .17 .16 .03 .05 .05 .46 .52
[1] 1i79.a .02
0
.04 .03 .04 .04 .03 .06 .04 .05 .02 .16 .16 .04 .05 .06 .45 .52
[1] 1i7b.a .03 .04
0
.07 .07 .07 .04 .07 .04 .07 .06 .17 .14 .05 .07 .07 .47 .52
[1] 1i7c.a .05 .03 .07
0
.01 .03 .05 .05 .07 .04 .02 .16 .18 .04 .05 .05 .45 .52
[1] 1i7m.a .05 .04 .07 .01
0
.04 .06 .06 .07 .05 .02 .17 .19 .05 .05 .06 .46 .52
[1] 3dz2.a .05 .04 .07 .03 .04
0
.07 .03 .07 .02 .03 .18 .20 .06 .03 .03 .48 .55
[1] 3dz3.a .03 .03 .04 .05 .06 .07
0
.08 .02 .07 .05 .15 .15 .05 .07 .08 .44 .50
[1] 3dz4.a .05 .06 .07 .05 .06 .03 .08
0
.08 .02 .03 .19 .20 .06 0 0 .49 .56
[1] 3dz5.a .03 .04 .04 .07 .07 .07 .02 .08
0
.07 .06 .14 .14 .07 .07 .08 .43 .50
[1] 3dz6.a .05 .05 .07 .04 .05 .02 .07 .02 .07
0
.03 .19 .21 .06 .02 .02 .48 .55
[1] 3dz7.a .04 .02 .06 .02 .02 .03 .05 .03 .06 .03
0
.16 .18 .03 .03 .03 .45 .52
[1] 3ep3.a .17 .16 .17 .16 .17 .18 .15 .19 .14 .19 .16
0
.03 .18 .19 .19 .30 .37
[1] 3ep6.a .16 .16 .14 .18 .19 .20 .15 .20 .14 .21 .18 .03
0
.18 .21 .20 .32 .38
[1] 3epb.a .03 .04 .05 .04 .05 .06 .05 .06 .07 .06 .03 .18 .18
0
.06 .06 .48 .53
[1] 3h0v.a .05 .05 .07 .05 .05 .03 .07 0 .07 .02 .03 .19 .21 .06
0
0 .48 .55
[1] 3h0w.a .05 .06 .07 .05 .06 .03 .08 0 .08 .02 .03 .19 .20 .06 0
0
.49 .56
[2] 1jl0.a .46 .45 .47 .45 .46 .48 .44 .49 .43 .48 .45 .30 .32 .48 .48 .49
0
.15
[2] 1msv.b .52 .52 .52 .52 .52 .55 .50 .56 .50 .55 .52 .37 .38 .53 .55 .56 .15
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 Å)

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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1i72.a
1i79.a
1i7b.a
1i7c.a
1i7m.a
3dz2.a
3dz3.a
3dz4.a
3dz5.a
3dz6.a
3dz7.a
3ep3.a
3ep6.a
3epb.a
3h0v.a
3h0w.a
1jl0.a
1msv.b
[1] 1i72.a
0
0.1 0.2 0.4 0.4 0.2 0.4 0.2 0.4 0.2 0.2 0.2 0.3 0.3 0.3 0.1 0.2 0.3
[1] 1i79.a 0.1
0
0.3 0.4 0.4 0.1 0.4 0.1 0.4 0.1 0.1 0.2 0.3 0.3 0.2 0.1 0.2 0.3
[1] 1i7b.a 0.2 0.3
0
0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.2 0.1 0.4 0.4 0.3 0.2 0.2
[1] 1i7c.a 0.4 0.4 0.3
0
0.3 0.4 0.3 0.4 0.3 0.4 0.4 0.4 0.3 0.6 0.4 0.4 0.3 0.3
[1] 1i7m.a 0.4 0.4 0.3 0.3
0
0.4 0.4 0.4 0.4 0.4 0.4 0.3 0.3 0.5 0.4 0.4 0.3 0.3
[1] 3dz2.a 0.2 0.1 0.3 0.4 0.4
0
0.4 0.1 0.5 0.1 0.1 0.2 0.3 0.4 0.2 0.1 0.2 0.3
[1] 3dz3.a 0.4 0.4 0.3 0.3 0.4 0.4
0
0.4 0.3 0.4 0.4 0.3 0.3 0.6 0.5 0.4 0.3 0.3
[1] 3dz4.a 0.2 0.1 0.3 0.4 0.4 0.1 0.4
0
0.4 0.1 0.1 0.2 0.3 0.4 0.2 0.1 0.2 0.3
[1] 3dz5.a 0.4 0.4 0.4 0.3 0.4 0.5 0.3 0.4
0
0.4 0.4 0.4 0.4 0.6 0.4 0.4 0.4 0.3
[1] 3dz6.a 0.2 0.1 0.3 0.4 0.4 0.1 0.4 0.1 0.4
0
0.1 0.2 0.3 0.3 0.2 0.1 0.2 0.3
[1] 3dz7.a 0.2 0.1 0.3 0.4 0.4 0.1 0.4 0.1 0.4 0.1
0
0.2 0.3 0.3 0.2 0.1 0.2 0.3
[1] 3ep3.a 0.2 0.2 0.2 0.4 0.3 0.2 0.3 0.2 0.4 0.2 0.2
0
0.2 0.3 0.3 0.2 0.2 0.2
[1] 3ep6.a 0.3 0.3 0.1 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.2
0
0.4 0.4 0.3 0.2 0.2
[1] 3epb.a 0.3 0.3 0.4 0.6 0.5 0.4 0.6 0.4 0.6 0.3 0.3 0.3 0.4
0
0.4 0.3 0.4 0.4
[1] 3h0v.a 0.3 0.2 0.4 0.4 0.4 0.2 0.5 0.2 0.4 0.2 0.2 0.3 0.4 0.4
0
0.2 0.3 0.4
[1] 3h0w.a 0.1 0.1 0.3 0.4 0.4 0.1 0.4 0.1 0.4 0.1 0.1 0.2 0.3 0.3 0.2
0
0.2 0.3
[2] 1jl0.a 0.2 0.2 0.2 0.3 0.3 0.2 0.3 0.2 0.4 0.2 0.2 0.2 0.2 0.4 0.3 0.2
0
0.8
[2] 1msv.b 0.3 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.2 0.2 0.4 0.4 0.3 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1i72.a
1i79.a
1i7b.a
1i7c.a
1i7m.a
3dz2.a
3dz3.a
3dz4.a
3dz5.a
3dz6.a
3dz7.a
3ep3.a
3ep6.a
3epb.a
3h0v.a
3h0w.a
1jl0.a
1msv.b
[1] 1i72.a
0
0.2 0.4 0.6 0.7 0.2 0.5 0.3 0.6 0.3 0.3 0.4 0.5 1.2 0.5 0.2 0.5 0.7
[1] 1i79.a 0.2
0
0.5 0.6 0.7 0.2 0.6 0.4 0.6 0.3 0.3 0.4 0.5 1.2 0.5 0.2 0.5 0.7
[1] 1i7b.a 0.4 0.5
0
0.7 0.8 0.5 0.7 0.4 0.7 0.5 0.5 0.5 0.2 1.2 0.5 0.5 0.6 0.8
[1] 1i7c.a 0.6 0.6 0.7
0
0.7 0.5 0.5 0.5 0.5 0.6 0.5 0.5 0.7 1.3 0.7 0.5 0.6 0.7
[1] 1i7m.a 0.7 0.7 0.8 0.7
0
0.7 0.7 0.7 0.8 0.8 0.8 0.7 0.8 1.3 0.8 0.7 0.7 0.5
[1] 3dz2.a 0.2 0.2 0.5 0.5 0.7
0
0.5 0.3 0.6 0.2 0.3 0.4 0.5 1.2 0.4 0.1 0.4 0.7
[1] 3dz3.a 0.5 0.6 0.7 0.5 0.7 0.5
0
0.6 0.3 0.6 0.6 0.6 0.7 1.3 0.7 0.5 0.6 0.6
[1] 3dz4.a 0.3 0.4 0.4 0.5 0.7 0.3 0.6
0
0.6 0.3 0.1 0.3 0.5 1.2 0.4 0.3 0.5 0.7
[1] 3dz5.a 0.6 0.6 0.7 0.5 0.8 0.6 0.3 0.6
0
0.6 0.6 0.6 0.7 1.4 0.7 0.5 0.6 0.7
[1] 3dz6.a 0.3 0.3 0.5 0.6 0.8 0.2 0.6 0.3 0.6
0
0.4 0.5 0.6 1.2 0.4 0.2 0.5 0.7
[1] 3dz7.a 0.3 0.3 0.5 0.5 0.8 0.3 0.6 0.1 0.6 0.4
0
0.3 0.5 1.2 0.4 0.3 0.5 0.7
[1] 3ep3.a 0.4 0.4 0.5 0.5 0.7 0.4 0.6 0.3 0.6 0.5 0.3
0
0.5 1.2 0.5 0.4 0.5 0.7
[1] 3ep6.a 0.5 0.5 0.2 0.7 0.8 0.5 0.7 0.5 0.7 0.6 0.5 0.5
0
1.2 0.5 0.5 0.7 0.8
[1] 3epb.a 1.2 1.2 1.2 1.3 1.3 1.2 1.3 1.2 1.4 1.2 1.2 1.2 1.2
0
1.2 1.2 0.8 1.3
[1] 3h0v.a 0.5 0.5 0.5 0.7 0.8 0.4 0.7 0.4 0.7 0.4 0.4 0.5 0.5 1.2
0
0.4 0.6 0.8
[1] 3h0w.a 0.2 0.2 0.5 0.5 0.7 0.1 0.5 0.3 0.5 0.2 0.3 0.4 0.5 1.2 0.4
0
0.4 0.7
[2] 1jl0.a 0.5 0.5 0.6 0.6 0.7 0.4 0.6 0.5 0.6 0.5 0.5 0.5 0.7 0.8 0.6 0.4
0
1.2
[2] 1msv.b 0.7 0.7 0.8 0.7 0.5 0.7 0.6 0.7 0.7 0.7 0.7 0.7 0.8 1.3 0.8 0.7 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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