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CTBP1_HUMAN_20_357

C-terminal-binding protein 1 [D-isomer specific 2-hydroxyacid dehydrogenase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CTBP1_HUMAN):R: Interaction with GLIS2 2 (315, 318, 327)
76, 77, 97:101, 123, 124, 266
76, 77, 97:101, 123, 124, 266, 315, 318, 327
Cofactors (cF):nad

Full PDB list

1hku, 1hl3, 1mx3, 2hu2, 3ga0, 4lce, 4u6q, 4u6s (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF
Y
7
6
H
7
7
R
9
7
I
9
8
G
9
9
S
1
0
0
G
1
0
1
R
2
6
6
H
3
1
5
W
3
1
8
M
3
2
7
[1]2hu2.a none . . . . . . . . . . . nad
[1]4lce.a kmt9 . . . . . . . . . . . nad
[1]4u6q.a 3cr13 . . . . . . . . . . .
[1]4u6s.a ppy12 . . . . . . . . . . . nad

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

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PDB.ch
A1 cF
Y
7
6
H
7
7
R
9
7
I
9
8
G
9
9
S
1
0
0
G
1
0
1
A
1
2
3
S
1
2
4
R
2
6
6
H
3
1
5
W
3
1
8
M
3
2
7
[1]2hu2.a . . . . . . . . . . . . . nad
[1]4lce.a . . . . . . . . . . . . . nad
[1]4u6q.a . . . . . . . . . . . . .
[1]4u6s.a . . . . . . . . . . . . . nad

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
2hu2.a is apo
4lce.a:kmt
4u6q.a:3cr
4u6s.a:ppy
[1] 2hu2.a
-
0.1 0.5 0.4
[1] 4lce.a -
0
0.4 0.1
[1] 4u6q.a - 0.1
0
0
[1] 4u6s.a - 0 0.1
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
2hu2.a
4lce.a
4u6q.a
4u6s.a
[1] 2hu2.a
0
.02 .05 .04
[1] 4lce.a .02
0
.04 .02
[1] 4u6q.a .05 .04
0
.02
[1] 4u6s.a .04 .02 .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
2hu2.a
4lce.a
4u6q.a
4u6s.a
[1] 2hu2.a
0
0.2 0.3 1.0
[1] 4lce.a 0.2
0
0.3 0.9
[1] 4u6q.a 0.3 0.3
0
0.9
[1] 4u6s.a 1.0 0.9 0.9
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
2hu2.a
4lce.a
4u6q.a
4u6s.a
[1] 2hu2.a
0
0.4 0.6 0.9
[1] 4lce.a 0.4
0
0.4 0.8
[1] 4u6q.a 0.6 0.4
0
0.7
[1] 4u6s.a 0.9 0.8 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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