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DCUP_HUMAN_2_367

Uroporphyrinogen decarboxylase [Uroporphyrinogen decarboxylase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DCUP_HUMAN):R: Substrate binding (37:41)
36, 46, 50, 55, 82:88, 100, 105, 106, 154, 156, 164, 170, 171, 217, 219, 220, 261, 339
36:41, 46, 50, 55, 82:88, 100, 105, 106, 154, 156, 164, 170, 171, 217, 219, 220, 261, 339

Full PDB list

1jph, 1jpi, 1jpk, 1r3q, 1r3r, 1r3s, 1r3t, 1r3v, 1r3w, 1r3y, 1uro, 2q6z, 2q71, 3gvq, 3gvr, 3gvv, 3gvw, 3gw0, 3gw3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
M
3
6
R
3
7
Q
3
8
A
3
9
G
4
0
R
4
1
F
4
6
R
5
0
F
5
5
I
8
2
I
8
3
F
8
4
S
8
5
D
8
6
I
8
7
L
8
8
M
1
0
0
P
1
0
6
F
1
5
4
Y
1
6
4
G
1
7
0
F
2
1
7
S
2
1
9
F
2
6
1
H
3
3
9
[1]1jpk.a none . . . . . . . . - . . . . . . . - . . . . . . . .
[1]1r3q.a 1cp48 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1r3r.a none . . . . . . . . . . . . . N . . . . . . . . . . .
[1]1r3s.a 1cp48 . . . . . . . . . . . . . G . . . . . . . . . . .
[1]1r3t.a cp348 . . . . . . . . . . . . . G . . . . . . . . . . .
[1]1r3v.a 1cp48 . . . . . . . . . . . . . E . . . . . . . . . . .
[1]1r3w.a cp348 . . . . . . . . . . . . . . . . . . . F . . . . .
[1]1r3y.a cp348 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gvr.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gvw.a none . . . . . . . . . . . . . . . . . . . . . Y . . .

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
M
3
6
R
3
7
Q
3
8
A
3
9
G
4
0
R
4
1
F
4
6
R
5
0
F
5
5
I
8
2
I
8
3
F
8
4
S
8
5
D
8
6
I
8
7
L
8
8
M
1
0
0
G
1
0
5
P
1
0
6
F
1
5
4
G
1
5
6
Y
1
6
4
G
1
7
0
S
1
7
1
F
2
1
7
S
2
1
9
H
2
2
0
F
2
6
1
H
3
3
9
[1]1jpk.a . . . . . . . . - . . . . . * . - - . . D . . . . . . . .
[1]1r3q.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1r3r.a . . . . . . . . . . . . . N . . . . . . . . . . . . . . .
[1]1r3s.a . . . . . . . . . . . . . G . . . . . . . . . . . . . . .
[1]1r3t.a . . . . . . . . . . . . . G . . . . . . . . . . . . . . .
[1]1r3v.a . . . . . . . . . . . . . E . . . . . . . . . . . . . . .
[1]1r3w.a . . . . . . . . . . . . . . . . . . . . . F . . . . . . .
[1]1r3y.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gvr.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gvw.a . . . . . . . . * . . . . . * . . . . . . . . . Y . . . .

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
1jpk.a is apo
1r3q.a:1cp
1r3r.a is apo
1r3s.a:1cp
1r3t.a:cp3
1r3v.a:1cp
1r3w.a:cp3
1r3y.a:cp3
3gvr.a is apo
3gvw.a is apo
[1] 1jpk.a
-
2.4 - 1.4 1.2 1.5 1.9 2.0 - -
[1] 1r3q.a -
0.1
- 0.3 0.3 0.6 0.1 0.6 - -
[1] 1r3r.a - 0.6
-
0.2 0.4 0.3 0.4 0.3 - -
[1] 1r3s.a - 0.4 -
0.1
0.5 0.3 0.3 0.2 - -
[1] 1r3t.a - 0.3 - 0.1
0.1
0.4 0.1 0.4 - -
[1] 1r3v.a - 1.1 - 0.6 0.5
0
0.5 0.5 - -
[1] 1r3w.a - 0.6 - 0.1 0.4 0.2
0.2
0.1 - -
[1] 1r3y.a - 0.5 - 0.2 0.4 0.1 0.1
0.2
- -
[1] 3gvr.a - 1.5 - 0.9 0.8 0.8 1.1 0.9
-
-
[1] 3gvw.a - 2.2 - 2.3 1.3 2.7 1.8 1.8 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
1jpk.a
1r3q.a
1r3r.a
1r3s.a
1r3t.a
1r3v.a
1r3w.a
1r3y.a
3gvr.a
3gvw.a
[1] 1jpk.a
0
.11 .09 .10 .10 .11 .10 .10 .09 .09
[1] 1r3q.a .11
0
.04 .03 .02 .06 .03 .03 .08 .13
[1] 1r3r.a .09 .04
0
.01 .02 .05 .03 .03 .06 .12
[1] 1r3s.a .10 .03 .01
0
.01 .05 .02 .02 .06 .12
[1] 1r3t.a .10 .02 .02 .01
0
.05 .02 .02 .07 .12
[1] 1r3v.a .11 .06 .05 .05 .05
0
.04 .03 .06 .15
[1] 1r3w.a .10 .03 .03 .02 .02 .04
0
.01 .06 .13
[1] 1r3y.a .10 .03 .03 .02 .02 .03 .01
0
.06 .13
[1] 3gvr.a .09 .08 .06 .06 .07 .06 .06 .06
0
.11
[1] 3gvw.a .09 .13 .12 .12 .12 .15 .13 .13 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1jpk.a
1r3q.a
1r3r.a
1r3s.a
1r3t.a
1r3v.a
1r3w.a
1r3y.a
3gvr.a
3gvw.a
[1] 1jpk.a
0
0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.8
[1] 1r3q.a 0.7
0
0.2 0.2 0.3 0.3 0.2 0.1 0.8 1.1
[1] 1r3r.a 0.7 0.2
0
0.2 0.3 0.3 0.2 0.2 0.7 1.1
[1] 1r3s.a 0.7 0.2 0.2
0
0.3 0.3 0.2 0.2 0.8 1.1
[1] 1r3t.a 0.7 0.3 0.3 0.3
0
0.5 0.3 0.3 0.8 1.1
[1] 1r3v.a 0.7 0.3 0.3 0.3 0.5
0
0.2 0.3 0.8 1.2
[1] 1r3w.a 0.7 0.2 0.2 0.2 0.3 0.2
0
0.2 0.8 1.1
[1] 1r3y.a 0.7 0.1 0.2 0.2 0.3 0.3 0.2
0
0.7 1.0
[1] 3gvr.a 0.7 0.8 0.7 0.8 0.8 0.8 0.8 0.7
0
0.7
[1] 3gvw.a 0.8 1.1 1.1 1.1 1.1 1.2 1.1 1.0 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1jpk.a
1r3q.a
1r3r.a
1r3s.a
1r3t.a
1r3v.a
1r3w.a
1r3y.a
3gvr.a
3gvw.a
[1] 1jpk.a
0
1.3 1.2 1.3 1.2 1.2 1.5 1.5 1.3 1.1
[1] 1r3q.a 1.3
0
0.7 1.0 1.1 1.0 1.0 1.0 1.3 1.7
[1] 1r3r.a 1.2 0.7
0
0.9 0.9 0.8 1.0 1.1 1.1 1.6
[1] 1r3s.a 1.3 1.0 0.9
0
0.5 0.7 0.4 0.5 1.2 1.9
[1] 1r3t.a 1.2 1.1 0.9 0.5
0
0.6 0.6 0.6 1.1 1.7
[1] 1r3v.a 1.2 1.0 0.8 0.7 0.6
0
0.6 0.7 1.1 1.8
[1] 1r3w.a 1.5 1.0 1.0 0.4 0.6 0.6
0
0.3 1.2 1.8
[1] 1r3y.a 1.5 1.0 1.1 0.5 0.6 0.7 0.3
0
1.2 1.8
[1] 3gvr.a 1.3 1.3 1.1 1.2 1.1 1.1 1.2 1.2
0
1.3
[1] 3gvw.a 1.1 1.7 1.6 1.9 1.7 1.8 1.8 1.8 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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