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RET2_HUMAN_2_134

Retinol-binding protein 2 [Calycin superfamily. Fatty-acid binding protein (FABP) family]

Composition of the binding site

Protein chains monomer
A1 (RET2_HUMAN):17, 20, 21, 26, 30, 34, 35, 37, 39, 41, 52, 54, 56, 58:61, 63, 65, 77, 78, 107, 109, 118, 12017, 20, 21, 26, 30, 34, 35, 37, 39, 41, 52, 54, 56, 58:61, 63, 65, 77, 78, 107, 109, 118, 120

Full PDB list

1opa, 1opb, 2rcq, 2rct, 4ede, 4eej, 4efg, 4exz, 4gkc, 4qyn, 4qyp, 4qzt, 4qzu, 4ruu, 4zcb, 4zgu, 4zh6, 4zh9, 4zj0, 4zr2, 5dg4, 5dpq, 5f58, 5f6b, 5f7g, 5faz, 5fen, 5ffh, 5u6g (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
7
Y
2
0
M
2
1
I
2
6
A
3
4
Q
3
9
K
4
1
T
5
2
T
5
4
S
5
6
F
5
8
R
5
9
N
6
0
Y
6
1
V
6
3
S
7
7
L
7
8
W
1
0
7
Q
1
0
9
L
1
1
8
L
1
2
0
[1]1opa.b none . . . . . . . . . . . . . . L G . . . . .
[1]1opb.b ret21 . . . . . . . . . . . . . . L G . . . . .
[1]2rcq.a none . . . . . . . . . . . . . . . . . . . . .
[1]4ede.b ret20 . W - . W . L V - . . W . . . . . . K . .
[1]4eej.a ret20 . W . . . . L V C . . W . . . . . . K . .
[1]4efg.b ret5 . W . . . . L V - . . W . . . . . . K . .
[1]4qyn.b rtl21 . . . . . . . . . . . . . . . . . . . . .
[1]4qyp.a ret21 . . . . . . . . . . . . . . . . . . . . .
[1]4ruu.b ret7 . . . . . . L . . . . . . . . . . . K . .
[1]4zgu.b none . . . . . . . . . . . . . W . . . . . . .
[1]4zj0.a ret6 . . . . . . L . . . . . . W . . . . K . .
[1]4zr2.b none . . . . . . L . . . . . . W . . . . K . .
[1]5dg4.a none . . . . . . . . . . . . . L . . . . . . .
[1]5f58.b ret20 . . . . . . L V . . . F . . . . . . K . .
[1]5f6b.a ret20 . W . . . . L V . . . Y . . . . . . K . .
[1]5f7g.b ret20 . W . . . L L V . . . Y . . . . . . K . .
[1]5faz.a ret20 . . . . . . L V . . . . . . . . . . K . .
[1]5fen.a ret20 . . . . . . L . C . . . . . . . . . K . .
[1]5ffh.b ret5 . W . . . . L V . . . W . . . . . . K . .
[1]5u6g.b ret20 . . . . . . D . . . . . . . . . . . K . .

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
F
1
7
Y
2
0
M
2
1
I
2
6
T
3
0
A
3
4
V
3
5
L
3
7
Q
3
9
K
4
1
T
5
2
T
5
4
S
5
6
F
5
8
R
5
9
N
6
0
Y
6
1
V
6
3
F
6
5
S
7
7
L
7
8
W
1
0
7
Q
1
0
9
L
1
1
8
L
1
2
0
[1]1opa.b . . . . . . . . . . . . . . . . . L . G . . . . .
[1]1opb.b . . . . . . . . . . . . . . . . . L . G . . . . .
[1]2rcq.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ede.b . W - . L W . . . L V - . . W . * . . . . . K . .
[1]4eej.a . W . . L . . . . L V C . . W . * . . . * . K . .
[1]4efg.b . W . . L . . . . L V - . . W . . . . . . . K . .
[1]4qyn.b . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4qyp.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ruu.b . . . . . . . . . L . . . . . . . . . . . . K . .
[1]4zgu.b . . . . . . . . . . . . . . . . W . . . * . . . .
[1]4zj0.a . . . . . . . . . L . . . . . . W . . . . . K . .
[1]4zr2.b . . . . . . . . . L . . . . . . W . . . * . K . .
[1]5dg4.a . . . . . . . . . . . . . . * . L . . . . . . . .
[1]5f58.b . . . . . . . . . L V . . . F . . . . . . . K . .
[1]5f6b.a . W . . . . . . . L V . . . Y . . . . . . . K . .
[1]5f7g.b . W . . . . . . L L V . . . Y . * . . . . . K . .
[1]5faz.a . . . . . . . . . L V . . . . . . . . . . . K . .
[1]5fen.a . . . . . . . . . L . C . . . . . . . . . . K . .
[1]5ffh.b . W . . . . . . . L V . . . W . . . . . . . K . .
[1]5u6g.b . . . . . . . . . D . . . . . . * . . . . . K . .

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
1opa.b is apo
1opb.b:ret
2rcq.a is apo
4ede.b:ret
4eej.a:ret
4efg.b:ret
4qyn.b:rtl
4qyp.a:ret
4ruu.b:ret
4zgu.b is apo
4zj0.a:ret
4zr2.b is apo
5dg4.a is apo
5f58.b:ret
5f6b.a:ret
5f7g.b:ret
5faz.a:ret
5fen.a:ret
5ffh.b:ret
5u6g.b:ret
[1] 1opa.b
-
0 - 0.3 0.5 0 0 0 0 - 0 - - 0.3 0.2 0.2 0.5 0.4 0 0.3
[1] 1opb.b -
0
- 0.6 0.7 0 0 0 0 - 0 - - 0.3 0.3 0.2 0.8 0.4 0 0.3
[1] 2rcq.a - 0.3
-
0.7 0.8 0.1 0.3 0.3 0.1 - 0.1 - - 1.5 0.4 0.3 0.8 1.5 0 0.7
[1] 4ede.b - 2.0 -
0.6
2.1 0.8 2.0 2.5 0.8 - 0.8 - - 3.0 1.2 1.5 1.3 3.3 0.4 2.0
[1] 4eej.a - 0.8 - 0.8
0.8
0.4 1.2 0.6 0.6 - 0.6 - - 1.8 0.6 0.3 1.4 2.7 0.1 0.8
[1] 4efg.b - 0.6 - 0.5 1.0
0.6
0.5 0.3 0.8 - 0.6 - - 1.2 0.4 0.4 1.1 1.7 0.2 0.9
[1] 4qyn.b - 0 - 0.6 0.7 0
0
0 0 - 0 - - 0.7 0.2 0.3 0.6 0.8 0.1 0.5
[1] 4qyp.a - 0.3 - 0.4 0.7 0 0.3
0.3
0 - 0 - - 1.0 0.2 0.2 0.4 0.8 0 0.4
[1] 4ruu.b - 0.8 - 0.8 0.8 0.6 0.4 0.5
0.6
- 0.6 - - 1.5 0.7 0.3 0.9 2.0 0.2 0.8
[1] 4zgu.b - 4.8 - 4.3 4.3 0.1 4.6 4.8 0.1
-
0.1 - - 5.4 4.1 4.5 4.0 5.2 0 4.7
[1] 4zj0.a - 1.3 - 0.6 0.9 0.6 0.9 0.7 0.8 -
0.6
- - 1.3 0.7 0.4 0.9 1.5 0.2 1.1
[1] 4zr2.b - 1.8 - 0.9 1.2 0.8 0.9 0.8 0.8 - 0.8
-
- 2.0 0.8 1.2 1.6 1.8 0.2 1.1
[1] 5dg4.a - 3.4 - 2.9 3.7 0 3.4 3.6 0 - 0 -
-
3.8 2.9 2.9 3.1 3.6 0 3.7
[1] 5f58.b - 0.6 - 0.6 1.0 0.6 0.3 0.3 0.6 - 0.6 - -
0.6
0.6 0.5 1.4 0.8 0.2 0.7
[1] 5f6b.a - 0.5 - 0.7 1.2 0.6 0.6 0.2 0.6 - 0.6 - - 1.9
0.6
0.4 0.7 2.3 0.4 1.0
[1] 5f7g.b - 0.7 - 0.9 1.5 0.8 0.7 0.4 0.8 - 0.8 - - 1.9 1.1
0.6
1.3 2.4 0.6 1.3
[1] 5faz.a - 0.8 - 0.8 0.9 0.6 0.6 0.5 0.6 - 0.6 - - 1.0 0.5 0.3
0.8
1.4 0.2 0.9
[1] 5fen.a - 0.6 - 0.5 0.8 0.6 0.1 0.1 0.6 - 0.6 - - 0.6 0.4 0.3 1.2
0.6
0.2 0.7
[1] 5ffh.b - 0.8 - 1.3 1.4 1.0 0.9 0.3 0.9 - 0.8 - - 2.1 1.0 0.8 1.2 2.5
0.6
1.3
[1] 5u6g.b - 1.0 - 0.9 1.2 0.7 0.6 0.4 1.0 - 0.8 - - 2.2 0.8 0.5 1.5 2.8 0.5
0.9
[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
1opa.b
1opb.b
2rcq.a
4ede.b
4eej.a
4efg.b
4qyn.b
4qyp.a
4ruu.b
4zgu.b
4zj0.a
4zr2.b
5dg4.a
5f58.b
5f6b.a
5f7g.b
5faz.a
5fen.a
5ffh.b
5u6g.b
[1] 1opa.b
0
.04 .07 .20 .17 .07 .05 .05 .10 .23 .08 .15 .18 .05 .10 .10 .07 .05 .13 .13
[1] 1opb.b .04
0
.07 .20 .15 .08 .01 .04 .10 .21 .09 .13 .18 .07 .11 .12 .08 .06 .13 .13
[1] 2rcq.a .07 .07
0
.18 .14 .11 .06 .06 .10 .18 .11 .14 .13 .08 .10 .11 .10 .08 .14 .11
[1] 4ede.b .20 .20 .18
0
.18 .16 .20 .20 .18 .32 .20 .23 .27 .18 .12 .11 .20 .18 .15 .13
[1] 4eej.a .17 .15 .14 .18
0
.13 .14 .14 .12 .22 .16 .19 .18 .15 .11 .12 .14 .16 .14 .10
[1] 4efg.b .07 .08 .11 .16 .13
0
.09 .09 .09 .27 .07 .13 .22 .05 .05 .06 .07 .06 .07 .12
[1] 4qyn.b .05 .01 .06 .20 .14 .09
0
.03 .10 .20 .08 .14 .17 .07 .10 .11 .07 .07 .13 .12
[1] 4qyp.a .05 .04 .06 .20 .14 .09 .03
0
.08 .21 .08 .12 .17 .07 .10 .12 .06 .07 .10 .10
[1] 4ruu.b .10 .10 .10 .18 .12 .09 .10 .08
0
.24 .05 .16 .20 .09 .06 .08 .03 .10 .08 .08
[1] 4zgu.b .23 .21 .18 .32 .22 .27 .20 .21 .24
0
.27 .27 .26 .25 .25 .26 .26 .24 .29 .21
[1] 4zj0.a .08 .09 .11 .20 .16 .07 .08 .08 .05 .27
0
.15 .22 .07 .08 .09 .02 .08 .10 .12
[1] 4zr2.b .15 .13 .14 .23 .19 .13 .14 .12 .16 .27 .15
0
.27 .10 .14 .16 .14 .10 .16 .14
[1] 5dg4.a .18 .18 .13 .27 .18 .22 .17 .17 .20 .26 .22 .27
0
.20 .20 .21 .22 .19 .25 .20
[1] 5f58.b .05 .07 .08 .18 .15 .05 .07 .07 .09 .25 .07 .10 .20
0
.08 .09 .07 .01 .12 .10
[1] 5f6b.a .10 .11 .10 .12 .11 .05 .10 .10 .06 .25 .08 .14 .20 .08
0
.02 .08 .09 .05 .08
[1] 5f7g.b .10 .12 .11 .11 .12 .06 .11 .12 .08 .26 .09 .16 .21 .09 .02
0
.09 .10 .04 .08
[1] 5faz.a .07 .08 .10 .20 .14 .07 .07 .06 .03 .26 .02 .14 .22 .07 .08 .09
0
.08 .09 .10
[1] 5fen.a .05 .06 .08 .18 .16 .06 .07 .07 .10 .24 .08 .10 .19 .01 .09 .10 .08
0
.12 .11
[1] 5ffh.b .13 .13 .14 .15 .14 .07 .13 .10 .08 .29 .10 .16 .25 .12 .05 .04 .09 .12
0
.09
[1] 5u6g.b .13 .13 .11 .13 .10 .12 .12 .10 .08 .21 .12 .14 .20 .10 .08 .08 .10 .11 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1opa.b
1opb.b
2rcq.a
4ede.b
4eej.a
4efg.b
4qyn.b
4qyp.a
4ruu.b
4zgu.b
4zj0.a
4zr2.b
5dg4.a
5f58.b
5f6b.a
5f7g.b
5faz.a
5fen.a
5ffh.b
5u6g.b
[1] 1opa.b
0
0.3 0.6 0.8 0.6 0.6 0.3 0.6 1.1 0.5 1.1 15 0.4 0.6 0.6 0.6 1.0 0.6 0.6 15
[1] 1opb.b 0.3
0
0.6 0.9 0.6 0.6 0.4 0.6 1.0 0.5 1.1 15 0.5 0.7 0.6 0.8 1.0 0.7 0.6 15
[1] 2rcq.a 0.6 0.6
0
1.1 0.7 0.8 0.5 0.6 1.1 0.4 1.4 15 0.5 0.9 0.8 0.8 1.2 0.9 0.8 15
[1] 4ede.b 0.8 0.9 1.1
0
0.7 0.8 0.8 1.1 1.4 1.0 1.5 14 0.9 0.9 0.7 0.7 1.4 0.8 0.8 14
[1] 4eej.a 0.6 0.6 0.7 0.7
0
0.6 0.6 0.8 1.2 0.7 1.3 15 0.7 0.7 0.5 0.6 1.2 0.8 0.6 15
[1] 4efg.b 0.6 0.6 0.8 0.8 0.6
0
0.6 0.8 1.0 0.8 1.2 15 0.7 0.6 0.3 0.6 1.1 0.7 0.3 15
[1] 4qyn.b 0.3 0.4 0.5 0.8 0.6 0.6
0
0.7 1.1 0.4 1.3 15 0.5 0.7 0.6 0.6 1.1 0.7 0.6 15
[1] 4qyp.a 0.6 0.6 0.6 1.1 0.8 0.8 0.7
0
1.1 0.6 1.2 15 0.6 0.9 0.8 0.9 1.1 0.9 0.8 15
[1] 4ruu.b 1.1 1.0 1.1 1.4 1.2 1.0 1.1 1.1
0
1.1 0.7 15 1.1 1.2 1.1 1.1 0.5 1.2 1.0 15
[1] 4zgu.b 0.5 0.5 0.4 1.0 0.7 0.8 0.4 0.6 1.1
0
1.3 15 0.4 0.8 0.7 0.8 1.1 0.9 0.8 15
[1] 4zj0.a 1.1 1.1 1.4 1.5 1.3 1.2 1.3 1.2 0.7 1.3
0
15 1.2 1.2 1.2 1.3 0.5 1.1 1.2 15
[1] 4zr2.b 15 15 15 14 15 15 15 15 15 15 15
0
15 15 15 15 15 15 15 8.1
[1] 5dg4.a 0.4 0.5 0.5 0.9 0.7 0.7 0.5 0.6 1.1 0.4 1.2 15
0
0.7 0.7 0.7 1.1 0.7 0.8 15
[1] 5f58.b 0.6 0.7 0.9 0.9 0.7 0.6 0.7 0.9 1.2 0.8 1.2 15 0.7
0
0.6 0.5 1.0 0.4 0.7 15
[1] 5f6b.a 0.6 0.6 0.8 0.7 0.5 0.3 0.6 0.8 1.1 0.7 1.2 15 0.7 0.6
0
0.5 1.0 0.7 0.3 15
[1] 5f7g.b 0.6 0.8 0.8 0.7 0.6 0.6 0.6 0.9 1.1 0.8 1.3 15 0.7 0.5 0.5
0
1.1 0.6 0.6 15
[1] 5faz.a 1.0 1.0 1.2 1.4 1.2 1.1 1.1 1.1 0.5 1.1 0.5 15 1.1 1.0 1.0 1.1
0
1.1 1.1 15
[1] 5fen.a 0.6 0.7 0.9 0.8 0.8 0.7 0.7 0.9 1.2 0.9 1.1 15 0.7 0.4 0.7 0.6 1.1
0
0.7 15
[1] 5ffh.b 0.6 0.6 0.8 0.8 0.6 0.3 0.6 0.8 1.0 0.8 1.2 15 0.8 0.7 0.3 0.6 1.1 0.7
0
15
[1] 5u6g.b 15 15 15 14 15 15 15 15 15 15 15 8.1 15 15 15 15 15 15 15
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
1opa.b
1opb.b
2rcq.a
4ede.b
4eej.a
4efg.b
4qyn.b
4qyp.a
4ruu.b
4zgu.b
4zj0.a
4zr2.b
5dg4.a
5f58.b
5f6b.a
5f7g.b
5faz.a
5fen.a
5ffh.b
5u6g.b
[1] 1opa.b
0
0.5 0.7 1.0 1.1 1.2 0.5 0.8 1.6 0.9 1.7 16 1.2 1.3 1.3 1.3 1.5 0.8 1.1 15
[1] 1opb.b 0.5
0
0.7 1.1 1.2 1.2 0.6 0.7 1.5 1.0 1.6 16 1.2 1.4 1.3 1.4 1.5 1.0 1.2 16
[1] 2rcq.a 0.7 0.7
0
1.1 1.2 1.3 0.7 0.8 1.5 0.8 1.7 16 1.2 1.5 1.4 1.4 1.6 1.1 1.3 15
[1] 4ede.b 1.0 1.1 1.1
0
1.3 1.1 1.1 1.2 1.9 1.2 1.9 15 0.9 1.1 0.9 0.9 1.9 1.2 1.1 14
[1] 4eej.a 1.1 1.2 1.2 1.3
0
1.0 1.2 1.4 2.0 1.3 2.1 15 1.2 1.0 0.8 0.8 2.0 1.3 0.9 15
[1] 4efg.b 1.2 1.2 1.3 1.1 1.0
0
1.2 1.4 1.9 1.4 2.1 15 1.3 0.9 0.7 0.8 1.9 1.2 0.5 15
[1] 4qyn.b 0.5 0.6 0.7 1.1 1.2 1.2
0
0.9 1.6 0.9 1.7 16 1.2 1.3 1.3 1.3 1.6 0.9 1.2 15
[1] 4qyp.a 0.8 0.7 0.8 1.2 1.4 1.4 0.9
0
1.4 1.1 1.5 16 0.8 1.6 1.5 1.5 1.4 1.2 1.4 16
[1] 4ruu.b 1.6 1.5 1.5 1.9 2.0 1.9 1.6 1.4
0
1.7 0.9 16 1.9 2.1 2.0 2.0 0.7 1.8 1.9 15
[1] 4zgu.b 0.9 1.0 0.8 1.2 1.3 1.4 0.9 1.1 1.7
0
2.1 16 1.2 1.5 1.4 1.4 1.7 1.2 1.4 15
[1] 4zj0.a 1.7 1.6 1.7 1.9 2.1 2.1 1.7 1.5 0.9 2.1
0
16 1.9 2.1 2.1 2.2 0.7 1.7 2.0 16
[1] 4zr2.b 16 16 16 15 15 15 16 16 16 16 16
0
16 16 15 15 16 16 15 8.2
[1] 5dg4.a 1.2 1.2 1.2 0.9 1.2 1.3 1.2 0.8 1.9 1.2 1.9 16
0
1.4 1.4 1.4 1.8 1.5 1.3 15
[1] 5f58.b 1.3 1.4 1.5 1.1 1.0 0.9 1.3 1.6 2.1 1.5 2.1 16 1.4
0
1.0 0.8 2.0 1.1 1.0 15
[1] 5f6b.a 1.3 1.3 1.4 0.9 0.8 0.7 1.3 1.5 2.0 1.4 2.1 15 1.4 1.0
0
0.7 2.0 1.4 0.6 15
[1] 5f7g.b 1.3 1.4 1.4 0.9 0.8 0.8 1.3 1.5 2.0 1.4 2.2 15 1.4 0.8 0.7
0
2.0 1.4 0.7 15
[1] 5faz.a 1.5 1.5 1.6 1.9 2.0 1.9 1.6 1.4 0.7 1.7 0.7 16 1.8 2.0 2.0 2.0
0
1.7 1.9 15
[1] 5fen.a 0.8 1.0 1.1 1.2 1.3 1.2 0.9 1.2 1.8 1.2 1.7 16 1.5 1.1 1.4 1.4 1.7
0
1.3 15
[1] 5ffh.b 1.1 1.2 1.3 1.1 0.9 0.5 1.2 1.4 1.9 1.4 2.0 15 1.3 1.0 0.6 0.7 1.9 1.3
0
15
[1] 5u6g.b 15 16 15 14 15 15 15 16 15 15 16 8.2 15 15 15 15 15 15 15
0
[Binding site full-atom RMSD matrix]







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