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PRP4B_HUMAN_656_1007

Serine/threonine-protein kinase PRP4 homolog [Protein kinase superfamily. CMGC Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PRP4B_HUMAN):D: Protein kinase (693, 695:699, 701, 703, 715, 717, 751, 767:773, 776, 819, 820, 822, 833, 834)693, 695:699, 701, 703, 715, 717, 751, 767:773, 776, 819, 820, 822, 833, 834

Full PDB list

4ian, 4ifc, 4iir, 4ijp

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
6
9
3
V
6
9
7
F
6
9
8
S
6
9
9
V
7
0
1
R
7
0
3
A
7
1
5
K
7
1
7
L
7
5
1
F
7
6
7
E
7
6
8
L
7
7
0
S
7
7
1
M
7
7
2
N
7
7
3
E
7
7
6
D
8
1
9
N
8
2
0
L
8
2
2
C
8
3
3
D
8
3
4
[1]4ian.a none . . . . . . . . . . . . . . . . . . . . .
[1]4ifc.a adp27 . . . . . . . . . . . . . . . . . . . . .
[1]4iir.a anp,mg32 . - - . . . . . . . . . . . . . . . . . .
[1]4iir.b anp31 . - - . . . . . . . . . . . . . . . . . .
[1]4ijp.b 1eh28 . . . . . . . . . . . . . . . . . . . . .

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
T
6
9
3
Q
6
9
5
G
6
9
6
V
6
9
7
F
6
9
8
S
6
9
9
V
7
0
1
R
7
0
3
A
7
1
5
K
7
1
7
L
7
5
1
F
7
6
7
E
7
6
8
P
7
6
9
L
7
7
0
S
7
7
1
M
7
7
2
N
7
7
3
E
7
7
6
D
8
1
9
N
8
2
0
L
8
2
2
C
8
3
3
D
8
3
4
[1]4ian.a . . * * * . . . . . . . . . . . . . . . . . . .
[1]4ifc.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4iir.a . . . - - . . . . . . . . . . . . . . . . . . .
[1]4iir.b . . - - - . . . . . . . . . . . . . . . . . . .
[1]4ijp.b . . . . . . . . . . . . . . . . . . . . . . . .

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
4ian.a is apo
4ifc.a:adp
4iir.a:anp,mg
4iir.b:anp
4ijp.b:1eh
[1] 4ian.a
-
3.2 4.6 3.2 0.4
[1] 4ifc.a -
0
0.2 0.1 0.2
[1] 4iir.a - 0.1
0
0 0.7
[1] 4iir.b - 0.1 0
0
0.6
[1] 4ijp.b - 0.7 0.6 0.7
0
[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
4ian.a
4ifc.a
4iir.a
4iir.b
4ijp.b
[1] 4ian.a
0
.24 .25 .25 .25
[1] 4ifc.a .24
0
.03 .02 .04
[1] 4iir.a .25 .03
0
0 .06
[1] 4iir.b .25 .02 0
0
.06
[1] 4ijp.b .25 .04 .06 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
4ian.a
4ifc.a
4iir.a
4iir.b
4ijp.b
[1] 4ian.a
0
1.2 1.4 0.8 1.2
[1] 4ifc.a 1.2
0
0.7 0.3 0.4
[1] 4iir.a 1.4 0.7
0
0.3 0.8
[1] 4iir.b 0.8 0.3 0.3
0
0.4
[1] 4ijp.b 1.2 0.4 0.8 0.4
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
4ian.a
4ifc.a
4iir.a
4iir.b
4ijp.b
[1] 4ian.a
0
1.8 1.5 1.1 1.9
[1] 4ifc.a 1.8
0
0.7 0.5 0.6
[1] 4iir.a 1.5 0.7
0
0.6 1.0
[1] 4iir.b 1.1 0.5 0.6
0
0.8
[1] 4ijp.b 1.9 0.6 1.0 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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