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CDC7_HUMAN_36_574

Cell division cycle 7-related protein kinase [Protein kinase superfamily. Ser/Thr protein kinase family. CDC7 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDC7_HUMAN):D: Protein kinase (64:67, 70, 72, 88, 90, 118, 134:137, 139, 181, 182, 184, 195, 196)64:67, 70, 72, 88, 90, 118, 134:137, 139, 181, 182, 184, 195, 196
Metals (Me):Mg

Full PDB list

4f99, 4f9a, 4f9b, 4f9c (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
6
4
G
6
5
E
6
6
G
6
7
S
7
0
V
7
2
A
8
8
K
9
0
M
1
1
8
M
1
3
4
P
1
3
5
Y
1
3
6
L
1
3
7
H
1
3
9
S
1
8
1
N
1
8
2
L
1
8
4
V
1
9
5
D
1
9
6
[1]4f9a.c adp27 . . . . . . . . . . . . . . . . . . . Mg
[1]4f9b.a 0sy16 . . . . . . . . . . . . . . . . . . .
[1]4f9c.a 0sx20 . . . . . . . . . . . . . . . . . . .

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 Me
I
6
4
G
6
5
E
6
6
G
6
7
S
7
0
V
7
2
A
8
8
K
9
0
M
1
1
8
M
1
3
4
P
1
3
5
Y
1
3
6
L
1
3
7
H
1
3
9
S
1
8
1
N
1
8
2
L
1
8
4
V
1
9
5
D
1
9
6
[1]4f9a.c . . . . . . . . . . . . . . . . . . . Mg
[1]4f9b.a . . . . . . . . . . . . . . . . . . .
[1]4f9c.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
4f9a.c:adp
4f9b.a:0sy
4f9c.a:0sx
[1] 4f9a.c
0
0 0
[1] 4f9b.a 0.5
0
0.2
[1] 4f9c.a 0.6 0
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
4f9a.c
4f9b.a
4f9c.a
[1] 4f9a.c
0
.04 .03
[1] 4f9b.a .04
0
.02
[1] 4f9c.a .03 .02
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

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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
4f9a.c
4f9b.a
4f9c.a
[1] 4f9a.c
0
0.4 0.5
[1] 4f9b.a 0.4
0
0.6
[1] 4f9c.a 0.5 0.6
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

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
4f9a.c
4f9b.a
4f9c.a
[1] 4f9a.c
0
0.5 0.6
[1] 4f9b.a 0.5
0
0.6
[1] 4f9c.a 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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