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NEK2_HUMAN_1_273

Serine/threonine-protein kinase Nek2 [Protein kinase superfamily. NEK Ser/Thr protein kinase family. NIMA subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NEK2_HUMAN):D: Protein kinase (12, 14:20, 22, 35, 37, 68, 70, 86:93, 96, 145, 146, 148, 158:164, 166)12, 14:20, 22, 35, 37, 68, 70, 86:93, 96, 145, 146, 148, 158:164, 166

Full PDB list

2jav, 2w5a, 2w5b, 2w5h, 2wqo, 2xk3, 2xk4, 2xk6, 2xk7, 2xk8, 2xkc, 2xkd, 2xke, 2xkf, 2xnm, 2xnn, 2xno, 2xnp, 4a4x, 4afe, 5m51, 5m53, 5m55, 5m57

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
2
I
1
4
G
1
5
T
1
6
G
1
7
S
1
8
Y
1
9
C
2
2
V
3
5
K
3
7
V
6
8
Y
7
0
M
8
6
E
8
7
Y
8
8
C
8
9
E
9
0
G
9
2
D
9
3
S
9
6
A
1
4
5
N
1
4
6
F
1
4
8
G
1
5
8
D
1
5
9
F
1
6
0
L
1
6
2
A
1
6
3
R
1
6
4
L
1
6
6
[1]2jav.a 5z523 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2w5a.a adp,mg28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2w5b.a ags,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2w5h.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]2wqo.a vgk28 . . . . - - - . . . . . . . . . . . . . . . . . . - - - - -
[1]2xk3.a xk323 . . . . - - - . . . . . . . . . . . . . . . . . . . - - - -
[1]2xk4.a ol231 . . . . - - . . . . . . . . . . . . . . . . . . . . . - - -
[1]2xk6.a eqh24 . . . - - - - . . . . . . . . . . . . . . . . . . - - - - -
[1]2xk7.a 30e30 . . . . - - - . . . . . . . . . . . . . . . . . . - - - - -
[1]2xk8.a 5r130 . . . . - - - . . . . . . . . . . . . . . . . . . . - - - -
[1]2xkc.a 4vq29 . . . . - - . . . . . . . . . . . . . . . . . . . - - - - -
[1]2xkd.a t3m28 . . . . - - - . . . . . . . . . . . . . . . . . . . - - - -
[1]2xke.a wi224 . . . . - - - . . . . . . . . . . . . . . . . . . . - - - -
[1]2xkf.a bx128 . . . . - - - . . . . . . . . . . . . . . . . . . . - - - -
[1]2xnm.a wgz38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2xnn.a 43030 . . . . - - . . . . . . . . . . . . . . . . . . . . - - - -
[1]2xno.a ed837 . . . . . . . . . . . . . . . . . . . . . . . . . . - - - -
[1]2xnp.a wcx39 . . . . . - . . . . . . . . . . . . . . . . . . . . . - - -
[1]4a4x.a jup38 . . . . . . . . . . . . . . . . . . . . . . . . . . . - - -
[1]4afe.a ggy34 . . . . . . . . . . . . . . . . . . . . . . . . . . . - - -
[1]5m55.a 7gg23 . . . . - - - . . . . . . . . . . . . . . . . . . - - - - -
[2]5m51.a nu627 . . . . . . . . . . . . . . . . . . . . . . . . . . - - - -
[2]5m53.a 7gj29 . . . . . . . . . . . . . . . . . . . . . . . . . . . - - -
[2]5m57.a 4sp28 . . . . . . . . . . . . . . . . . . . . . . . . . . - - - -

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
Y
1
2
I
1
4
G
1
5
T
1
6
G
1
7
S
1
8
Y
1
9
G
2
0
C
2
2
V
3
5
K
3
7
V
6
8
Y
7
0
M
8
6
E
8
7
Y
8
8
C
8
9
E
9
0
G
9
1
G
9
2
D
9
3
S
9
6
A
1
4
5
N
1
4
6
F
1
4
8
G
1
5
8
D
1
5
9
F
1
6
0
G
1
6
1
L
1
6
2
A
1
6
3
R
1
6
4
L
1
6
6
[1]2jav.a . . . . . . * . . . * . . . . . . . . . . . . . . . . . . * . . *
[1]2w5a.a . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . * .
[1]2w5b.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]2w5h.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . -
[1]2wqo.a . . . . - - - . . . . . . . . . . . . . . . . . . . . - - - - - -
[1]2xk3.a . . . . - - - - . . . . . . . . . . . . . . . . . . . * . - - - -
[1]2xk4.a . . . . - - . . . . . . . . . . . . . . . . . . . . . * . . - - -
[1]2xk6.a . . . - - - - - . . . . . . . . . . . . . . . . . . . - - - - - -
[1]2xk7.a . . . . - - - . . . . . . . . . . . . . . . . . . . . - - - - - -
[1]2xk8.a . . . . - - - - . . . . . . . . . . . . . . . . . . . * - - - - -
[1]2xkc.a . . . . - - . . . . . . . . . . . . . . . . . . . . . - - - - - -
[1]2xkd.a . . . . - - - . . . . . . . . . . . . . . . . . . . * . - - - - -
[1]2xke.a . . . . - - - . . . . . . . . . . . . . . . . . . . * . - - - - -
[1]2xkf.a . . . . - - - . . . . . . . . . . . . . . . . . . . . . - - - - -
[1]2xnm.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . . * * . .
[1]2xnn.a . . . . - - . . . . * . . . . . . . . . . . . . . . . . . - - - -
[1]2xno.a . . . . . . . . . . * . . . . . . . . . . . . . . . . . - - - - -
[1]2xnp.a . . . . . - . . . . . . . . . . . . . . . . . . . . . * . . - - -
[1]4a4x.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . - - -
[1]4afe.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . - - -
[1]5m55.a . . . . - - - - . . * . . . . . . . . . . . . . . . . - - - - - -
[2]5m51.a . . . . . * * . . . * . . . . . . . . . . . . . . . * . - - - - -
[2]5m53.a . . . . . . * . . . * . . . . . . . . . . . . . . . * . . . - - -
[2]5m57.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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2jav.a:5z5
2w5a.a:adp,mg
2w5b.a:ags,mg
2w5h.a is apo
2wqo.a:vgk
2xk3.a:xk3
2xk4.a:ol2
2xk6.a:eqh
2xk7.a:30e
2xk8.a:5r1
2xkc.a:4vq
2xkd.a:t3m
2xke.a:wi2
2xkf.a:bx1
2xnm.a:wgz
2xnn.a:430
2xno.a:ed8
2xnp.a:wcx
4a4x.a:jup
4afe.a:ggy
5m55.a:7gg
5m51.a:nu6
5m53.a:7gj
5m57.a:4sp
[1] 2jav.a
0
0.7 2.3 - 1.7 1.7 1.4 1.9 2.7 2.5 2.7 2.0 2.2 1.8 0.5 1.2 0.7 0.8 0.6 1.4 0.2 0.9 0.6 0.3
[1] 2w5a.a 0.8
0.1
1.2 - 2.7 2.9 2.6 3.2 3.8 2.5 2.8 3.1 3.3 2.8 1.1 2.1 2.0 1.4 1.2 2.2 0 0.2 0.3 0.3
[1] 2w5b.a 0.2 0
0
- 1.1 0.8 1.3 1.5 2.2 1.4 2.2 1.4 1.5 1.1 0.9 0.8 0.7 0.6 1.1 0.9 0.1 0.2 0.3 0.2
[1] 2w5h.a 0.2 0 0
-
0.4 0.4 1.0 1.2 0.8 0.5 1.1 0.6 0.8 1.0 0.5 0.7 0.5 0.6 1.0 0.4 0 0.1 0.2 0.2
[1] 2wqo.a 0.4 0.4 0.4 -
0
0 0.7 0.3 0.2 0.2 0.1 0 0 0.1 0.2 0.1 0.6 0.7 0.7 0.7 0.1 0.3 0.3 0.3
[1] 2xk3.a 0.2 1.5 1.5 - 0.1
0.2
0.4 0.5 0.2 0.1 0.1 0.1 0.1 0.2 0.3 0.5 0.6 0.5 0.9 0.8 0.1 0.2 0.3 0.4
[1] 2xk4.a 0.3 1.2 1.4 - 0.2 0.3
0
0.3 0.4 0.3 0.2 0.3 0.3 0.3 0.3 0.2 0.2 0.1 0.5 0.2 0.2 0.4 0.2 0.4
[1] 2xk6.a 0.1 0.1 0.1 - 0.1 0 0.1
0
0.5 0.2 0.2 0 0.1 0.1 0.1 0.1 0.3 0 0 0.2 0.1 0.3 0.2 0.3
[1] 2xk7.a 0.1 0 0 - 0 0 0.1 0
0
0 0 0 0.1 0.1 0.2 0.3 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.3
[1] 2xk8.a 0.4 2.8 3.5 - 0.1 0.1 0.8 0.4 0.4
0
0 0 0.1 0.2 1.5 1.8 1.5 1.5 1.7 1.5 0.1 0.7 0.3 2.2
[1] 2xkc.a 0.6 0 0.1 - 0.1 0.1 0.1 0.2 0.2 0
0
0 0.2 0.3 0.2 0.1 0.1 0.2 0.4 0.1 0.1 0.3 0.2 0.3
[1] 2xkd.a 0.4 0.9 0.2 - 0.1 0 0.9 0.3 0.4 0.3 0.2
0
0 0 0.6 0.4 0.6 0.8 1.0 0.6 0.1 0.2 0.2 0.3
[1] 2xke.a 0.1 0.5 0.5 - 0.1 0 1.0 0.2 0.3 0.1 0.3 0.1
0
0 0.2 0.3 0.3 0.5 0.6 0.4 0.1 0.3 0.3 0.3
[1] 2xkf.a 0.1 0.2 0.3 - 0.2 0 0.6 0.3 0.3 0.6 0.3 0.4 0.2
0
0.2 0.4 0.5 0.6 0.8 0.4 0.1 0.2 0.1 0.3
[1] 2xnm.a 0.1 1.9 4.9 - 1.0 0.7 0.5 1.0 2.2 1.1 1.6 1.0 1.4 0.9
0.2
0.3 0.3 0.3 0.3 0.3 0.1 0.2 0.2 0.3
[1] 2xnn.a 0.1 0 0.2 - 0.5 0.5 0.5 0.4 1.7 0.8 0.7 0.7 0.7 0.3 0.1
0.2
0.4 0.1 0.2 0.4 0.1 0.2 0.3 0.3
[1] 2xno.a 0.2 0.1 0 - 0.7 0.7 0.4 0.4 1.8 0.9 0.9 0.7 0.7 0.4 0.1 0.3
0.1
0.1 0.2 0.3 0.1 0.3 0.2 0.3
[1] 2xnp.a 0.3 1.2 2.1 - 0.4 0.4 0.2 0.6 0.8 0.2 0.4 0.5 0.4 0.4 0.1 0.2 0.3
0
0.1 0.3 0.2 0.3 0.4 0.4
[1] 4a4x.a 0.4 1.0 1.6 - 0.2 0.2 0.1 0.3 0.3 0.1 0.1 0.1 0.2 0.2 0 0.2 0.3 0
0
0.1 0.3 0.4 0.3 0.5
[1] 4afe.a 0.4 1.4 2.0 - 0.2 0.1 0.1 0.3 0.2 0.1 0.1 0.1 0.2 0.2 0 0.1 0.3 0 0
0.1
0.1 0.4 0.4 0.5
[1] 5m55.a 0.2 0.6 0.4 - 0.4 0.5 1.3 0.6 1.4 0.5 0.5 0.4 0.4 0.5 0.6 0.5 0.7 1.0 1.1 1.1
0
0.1 0.3 0.1
[2] 5m51.a 1.9 2.8 3.3 - 3.0 3.3 4.8 2.9 3.9 3.8 3.3 3.0 3.1 3.0 3.6 3.1 3.5 4.0 4.5 4.9 0.1
0
0.1 0.1
[2] 5m53.a 2.1 2.9 2.8 - 2.6 3.2 5.2 3.0 4.3 4.1 3.6 2.6 2.9 3.2 4.5 3.2 3.6 5.1 5.3 5.0 0.1 0
0
0.2
[2] 5m57.a 1.2 2.8 2.6 - 2.6 2.7 4.2 2.8 4.0 3.4 3.1 2.6 3.0 3.0 3.5 2.5 3.2 4.0 4.2 4.7 0 0.1 0.2
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2jav.a
2w5a.a
2w5b.a
2w5h.a
2wqo.a
2xk3.a
2xk4.a
2xk6.a
2xk7.a
2xk8.a
2xkc.a
2xkd.a
2xke.a
2xkf.a
2xnm.a
2xnn.a
2xno.a
2xnp.a
4a4x.a
4afe.a
5m55.a
5m51.a
5m53.a
5m57.a
[1] 2jav.a
0
.22 .17 .22 .22 .22 .21 .18 .17 .30 .19 .22 .22 .19 .21 .13 .12 .21 .19 .20 .17 .28 .29 .27
[1] 2w5a.a .22
0
.15 .20 .17 .21 .21 .18 .16 .26 .18 .16 .16 .15 .24 .12 .12 .22 .22 .23 .11 .18 .20 .19
[1] 2w5b.a .17 .15
0
.06 .14 .11 .11 .13 .11 .18 .12 .13 .15 .13 .22 .07 .07 .14 .13 .14 .08 .23 .24 .23
[1] 2w5h.a .22 .20 .06
0
.10 .06 .07 .08 .07 .13 .08 .09 .11 .10 .27 .11 .12 .09 .07 .09 .11 .28 .28 .27
[1] 2wqo.a .22 .17 .14 .10
0
.08 .09 .05 .06 .13 .04 .02 .02 .04 .25 .09 .10 .11 .10 .11 .07 .27 .27 .25
[1] 2xk3.a .22 .21 .11 .06 .08
0
.03 .06 .06 .09 .08 .08 .09 .09 .27 .10 .12 .05 .06 .05 .11 .31 .31 .29
[1] 2xk4.a .21 .21 .11 .07 .09 .03
0
.08 .08 .09 .07 .09 .11 .09 .27 .10 .11 .05 .05 .03 .10 .30 .31 .28
[1] 2xk6.a .18 .18 .13 .08 .05 .06 .08
0
.02 .15 .05 .05 .05 .04 .22 .07 .07 .11 .08 .09 .08 .28 .28 .26
[1] 2xk7.a .17 .16 .11 .07 .06 .06 .08 .02
0
.14 .04 .06 .06 .05 .21 .06 .06 .09 .08 .09 .07 .27 .28 .25
[1] 2xk8.a .30 .26 .18 .13 .13 .09 .09 .15 .14
0
.13 .13 .15 .15 .34 .17 .19 .11 .13 .11 .16 .36 .36 .34
[1] 2xkc.a .19 .18 .12 .08 .04 .08 .07 .05 .04 .13
0
.04 .06 .05 .24 .07 .08 .11 .08 .09 .07 .27 .26 .25
[1] 2xkd.a .22 .16 .13 .09 .02 .08 .09 .05 .06 .13 .04
0
.03 .04 .26 .09 .10 .11 .10 .11 .05 .25 .25 .23
[1] 2xke.a .22 .16 .15 .11 .02 .09 .11 .05 .06 .15 .06 .03
0
.04 .26 .09 .11 .12 .12 .13 .07 .26 .26 .24
[1] 2xkf.a .19 .15 .13 .10 .04 .09 .09 .04 .05 .15 .05 .04 .04
0
.23 .07 .08 .11 .10 .11 .05 .25 .25 .23
[1] 2xnm.a .21 .24 .22 .27 .25 .27 .27 .22 .21 .34 .24 .26 .26 .23
0
.18 .17 .29 .28 .29 .21 .37 .38 .37
[1] 2xnn.a .13 .12 .07 .11 .09 .10 .10 .07 .06 .17 .07 .09 .09 .07 .18
0
.03 .13 .12 .13 .04 .22 .22 .21
[1] 2xno.a .12 .12 .07 .12 .10 .12 .11 .07 .06 .19 .08 .10 .11 .08 .17 .03
0
.13 .12 .13 .06 .23 .23 .23
[1] 2xnp.a .21 .22 .14 .09 .11 .05 .05 .11 .09 .11 .11 .11 .12 .11 .29 .13 .13
0
.03 .03 .12 .28 .28 .27
[1] 4a4x.a .19 .22 .13 .07 .10 .06 .05 .08 .08 .13 .08 .10 .12 .10 .28 .12 .12 .03
0
.02 .13 .29 .29 .28
[1] 4afe.a .20 .23 .14 .09 .11 .05 .03 .09 .09 .11 .09 .11 .13 .11 .29 .13 .13 .03 .02
0
.13 .30 .30 .28
[1] 5m55.a .17 .11 .08 .11 .07 .11 .10 .08 .07 .16 .07 .05 .07 .05 .21 .04 .06 .12 .13 .13
0
.20 .21 .18
[2] 5m51.a .28 .18 .23 .28 .27 .31 .30 .28 .27 .36 .27 .25 .26 .25 .37 .22 .23 .28 .29 .30 .20
0
.08 .05
[2] 5m53.a .29 .20 .24 .28 .27 .31 .31 .28 .28 .36 .26 .25 .26 .25 .38 .22 .23 .28 .29 .30 .21 .08
0
.06
[2] 5m57.a .27 .19 .23 .27 .25 .29 .28 .26 .25 .34 .25 .23 .24 .23 .37 .21 .23 .27 .28 .28 .18 .05 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
2jav.a
2w5a.a
2w5b.a
2w5h.a
2wqo.a
2xk3.a
2xk4.a
2xk6.a
2xk7.a
2xk8.a
2xkc.a
2xkd.a
2xke.a
2xkf.a
2xnm.a
2xnn.a
2xno.a
2xnp.a
4a4x.a
4afe.a
5m55.a
5m51.a
5m53.a
5m57.a
[1] 2jav.a
0
2.6 2.7 2.3 0.9 1.7 1.7 0.9 0.9 1.7 1.1 1.1 1.1 1.1 2.6 1.8 1.1 1.7 1.8 1.8 1.2 1.7 2.2 1.7
[1] 2w5a.a 2.6
0
1.5 1.0 0.7 1.4 1.8 0.6 0.6 0.8 0.7 0.7 0.7 0.8 3.1 0.9 0.9 1.9 2.1 2.0 0.7 1.1 1.5 1.1
[1] 2w5b.a 2.7 1.5
0
0.3 0.7 1.3 1.6 0.7 0.7 0.8 0.7 0.8 0.9 0.9 2.6 1.1 1.0 1.7 1.8 1.8 0.8 1.3 1.4 1.2
[1] 2w5h.a 2.3 1.0 0.3
0
0.7 1.3 1.6 0.7 0.7 0.8 0.7 0.9 0.9 0.9 2.2 1.1 1.0 1.7 1.9 1.8 0.7 1.3 1.4 1.2
[1] 2wqo.a 0.9 0.7 0.7 0.7
0
0.5 0.6 0.6 0.6 0.5 0.6 0.4 0.3 0.5 0.7 0.6 0.7 0.6 0.6 0.6 0.8 0.9 1.0 0.9
[1] 2xk3.a 1.7 1.4 1.3 1.3 0.5
0
0.6 0.4 0.5 0.8 0.6 1.0 0.8 1.0 1.2 1.6 0.8 0.6 0.7 0.6 0.8 1.1 1.3 1.1
[1] 2xk4.a 1.7 1.8 1.6 1.6 0.6 0.6
0
0.5 0.4 1.0 0.7 1.0 0.8 0.9 2.1 1.7 0.8 0.5 0.5 0.5 0.8 1.2 1.7 1.2
[1] 2xk6.a 0.9 0.6 0.7 0.7 0.6 0.4 0.5
0
0.3 0.5 0.5 0.4 0.6 0.4 0.5 0.4 0.5 0.5 0.5 0.5 0.6 0.9 1.0 0.8
[1] 2xk7.a 0.9 0.6 0.7 0.7 0.6 0.5 0.4 0.3
0
0.5 0.5 0.5 0.6 0.5 0.6 0.5 0.5 0.5 0.5 0.5 0.5 0.9 1.0 0.9
[1] 2xk8.a 1.7 0.8 0.8 0.8 0.5 0.8 1.0 0.5 0.5
0
0.4 1.0 0.9 1.1 0.6 0.5 0.8 0.9 1.1 1.0 0.5 1.2 1.1 1.1
[1] 2xkc.a 1.1 0.7 0.7 0.7 0.6 0.6 0.7 0.5 0.5 0.4
0
0.5 0.6 0.5 1.2 0.5 0.7 0.8 0.8 0.7 0.5 0.9 0.9 0.8
[1] 2xkd.a 1.1 0.7 0.8 0.9 0.4 1.0 1.0 0.4 0.5 1.0 0.5
0
0.6 0.4 1.1 0.9 0.8 1.0 1.1 1.0 0.7 0.9 0.9 0.8
[1] 2xke.a 1.1 0.7 0.9 0.9 0.3 0.8 0.8 0.6 0.6 0.9 0.6 0.6
0
0.5 1.0 0.8 0.9 0.9 0.9 0.9 0.7 0.9 0.9 0.8
[1] 2xkf.a 1.1 0.8 0.9 0.9 0.5 1.0 0.9 0.4 0.5 1.1 0.5 0.4 0.5
0
1.1 0.9 0.8 0.9 1.0 0.9 0.7 0.9 1.0 0.8
[1] 2xnm.a 2.6 3.1 2.6 2.2 0.7 1.2 2.1 0.5 0.6 0.6 1.2 1.1 1.0 1.1
0
1.1 1.1 2.0 2.2 2.2 0.5 2.3 2.6 2.3
[1] 2xnn.a 1.8 0.9 1.1 1.1 0.6 1.6 1.7 0.4 0.5 0.5 0.5 0.9 0.8 0.9 1.1
0
0.6 1.7 1.8 1.7 0.4 1.1 1.6 1.1
[1] 2xno.a 1.1 0.9 1.0 1.0 0.7 0.8 0.8 0.5 0.5 0.8 0.7 0.8 0.9 0.8 1.1 0.6
0
0.8 0.9 0.9 0.6 1.6 1.6 1.6
[1] 2xnp.a 1.7 1.9 1.7 1.7 0.6 0.6 0.5 0.5 0.5 0.9 0.8 1.0 0.9 0.9 2.0 1.7 0.8
0
0.4 0.4 0.7 1.5 1.8 1.5
[1] 4a4x.a 1.8 2.1 1.8 1.9 0.6 0.7 0.5 0.5 0.5 1.1 0.8 1.1 0.9 1.0 2.2 1.8 0.9 0.4
0
0.2 0.8 1.8 2.1 1.8
[1] 4afe.a 1.8 2.0 1.8 1.8 0.6 0.6 0.5 0.5 0.5 1.0 0.7 1.0 0.9 0.9 2.2 1.7 0.9 0.4 0.2
0
0.7 1.7 2.0 1.7
[1] 5m55.a 1.2 0.7 0.8 0.7 0.8 0.8 0.8 0.6 0.5 0.5 0.5 0.7 0.7 0.7 0.5 0.4 0.6 0.7 0.8 0.7
0
0.8 0.9 0.8
[2] 5m51.a 1.7 1.1 1.3 1.3 0.9 1.1 1.2 0.9 0.9 1.2 0.9 0.9 0.9 0.9 2.3 1.1 1.6 1.5 1.8 1.7 0.8
0
0.5 0.4
[2] 5m53.a 2.2 1.5 1.4 1.4 1.0 1.3 1.7 1.0 1.0 1.1 0.9 0.9 0.9 1.0 2.6 1.6 1.6 1.8 2.1 2.0 0.9 0.5
0
0.5
[2] 5m57.a 1.7 1.1 1.2 1.2 0.9 1.1 1.2 0.8 0.9 1.1 0.8 0.8 0.8 0.8 2.3 1.1 1.6 1.5 1.8 1.7 0.8 0.4 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
2jav.a
2w5a.a
2w5b.a
2w5h.a
2wqo.a
2xk3.a
2xk4.a
2xk6.a
2xk7.a
2xk8.a
2xkc.a
2xkd.a
2xke.a
2xkf.a
2xnm.a
2xnn.a
2xno.a
2xnp.a
4a4x.a
4afe.a
5m55.a
5m51.a
5m53.a
5m57.a
[1] 2jav.a
0
3.6 3.6 3.3 2.2 2.9 3.0 2.0 1.4 3.2 1.4 2.5 2.4 2.4 3.0 1.8 1.4 2.8 2.8 2.8 1.4 2.2 2.6 2.2
[1] 2w5a.a 3.6
0
2.4 2.0 1.9 2.4 2.7 1.9 1.1 2.6 1.1 2.3 2.3 2.4 3.4 1.1 1.1 2.7 2.8 2.8 1.2 2.2 2.4 2.2
[1] 2w5b.a 3.6 2.4
0
0.3 1.9 2.4 2.6 1.9 1.3 2.3 1.2 2.5 2.5 2.5 3.2 1.4 1.3 2.6 2.8 2.7 1.0 2.6 2.6 2.5
[1] 2w5h.a 3.3 2.0 0.3
0
1.9 2.4 2.6 1.9 1.3 2.3 1.2 2.5 2.5 2.5 2.7 1.4 1.4 2.6 2.8 2.7 1.0 2.6 2.6 2.6
[1] 2wqo.a 2.2 1.9 1.9 1.9
0
1.0 1.0 1.0 1.8 0.9 1.6 0.7 0.6 0.7 1.9 1.9 1.9 1.7 1.7 1.7 1.9 2.0 2.1 2.0
[1] 2xk3.a 2.9 2.4 2.4 2.4 1.0
0
0.8 0.7 1.6 1.0 1.7 2.0 1.9 2.0 2.0 2.0 1.7 1.6 1.6 1.7 1.9 2.7 2.7 2.6
[1] 2xk4.a 3.0 2.7 2.6 2.6 1.0 0.8
0
0.8 1.4 1.1 1.6 2.1 2.0 2.0 2.6 2.0 1.6 1.4 1.4 1.4 1.8 2.6 2.9 2.6
[1] 2xk6.a 2.0 1.9 1.9 1.9 1.0 0.7 0.8
0
1.6 0.6 1.7 1.0 1.0 1.0 1.7 1.7 1.6 1.6 1.6 1.7 1.8 2.2 2.3 2.2
[1] 2xk7.a 1.4 1.1 1.3 1.3 1.8 1.6 1.4 1.6
0
1.6 0.8 1.8 1.8 1.8 1.0 0.9 0.8 0.8 0.8 0.8 1.1 1.5 1.6 1.5
[1] 2xk8.a 3.2 2.6 2.3 2.3 0.9 1.0 1.1 0.6 1.6
0
1.6 2.4 2.3 2.4 1.9 1.7 1.7 1.8 1.8 1.8 1.7 3.0 3.0 3.0
[1] 2xkc.a 1.4 1.1 1.2 1.2 1.6 1.7 1.6 1.7 0.8 1.6
0
1.8 1.8 1.8 1.4 0.9 1.1 0.9 0.9 1.0 1.0 1.4 1.6 1.4
[1] 2xkd.a 2.5 2.3 2.5 2.5 0.7 2.0 2.1 1.0 1.8 2.4 1.8
0
0.8 0.7 2.8 2.0 2.0 2.6 2.5 2.6 1.9 2.0 2.0 1.9
[1] 2xke.a 2.4 2.3 2.5 2.5 0.6 1.9 2.0 1.0 1.8 2.3 1.8 0.8
0
0.6 2.7 2.0 1.9 2.5 2.5 2.5 1.9 1.9 2.0 1.9
[1] 2xkf.a 2.4 2.4 2.5 2.5 0.7 2.0 2.0 1.0 1.8 2.4 1.8 0.7 0.6
0
2.7 2.0 1.9 2.5 2.5 2.5 1.9 1.9 2.0 1.9
[1] 2xnm.a 3.0 3.4 3.2 2.7 1.9 2.0 2.6 1.7 1.0 1.9 1.4 2.8 2.7 2.7
0
1.0 1.1 2.2 2.4 2.4 0.9 2.9 3.1 2.9
[1] 2xnn.a 1.8 1.1 1.4 1.4 1.9 2.0 2.0 1.7 0.9 1.7 0.9 2.0 2.0 2.0 1.0
0
0.6 1.5 1.6 1.6 0.9 1.6 1.8 1.5
[1] 2xno.a 1.4 1.1 1.3 1.4 1.9 1.7 1.6 1.6 0.8 1.7 1.1 2.0 1.9 1.9 1.1 0.6
0
1.0 1.1 1.1 0.9 1.8 1.9 1.8
[1] 2xnp.a 2.8 2.7 2.6 2.6 1.7 1.6 1.4 1.6 0.8 1.8 0.9 2.6 2.5 2.5 2.2 1.5 1.0
0
0.7 0.8 1.2 2.5 2.8 2.4
[1] 4a4x.a 2.8 2.8 2.8 2.8 1.7 1.6 1.4 1.6 0.8 1.8 0.9 2.5 2.5 2.5 2.4 1.6 1.1 0.7
0
0.6 1.2 2.6 2.9 2.5
[1] 4afe.a 2.8 2.8 2.7 2.7 1.7 1.7 1.4 1.7 0.8 1.8 1.0 2.6 2.5 2.5 2.4 1.6 1.1 0.8 0.6
0
1.3 2.6 2.8 2.5
[1] 5m55.a 1.4 1.2 1.0 1.0 1.9 1.9 1.8 1.8 1.1 1.7 1.0 1.9 1.9 1.9 0.9 0.9 0.9 1.2 1.2 1.3
0
1.4 1.5 1.4
[2] 5m51.a 2.2 2.2 2.6 2.6 2.0 2.7 2.6 2.2 1.5 3.0 1.4 2.0 1.9 1.9 2.9 1.6 1.8 2.5 2.6 2.6 1.4
0
0.9 0.4
[2] 5m53.a 2.6 2.4 2.6 2.6 2.1 2.7 2.9 2.3 1.6 3.0 1.6 2.0 2.0 2.0 3.1 1.8 1.9 2.8 2.9 2.8 1.5 0.9
0
0.9
[2] 5m57.a 2.2 2.2 2.5 2.6 2.0 2.6 2.6 2.2 1.5 3.0 1.4 1.9 1.9 1.9 2.9 1.5 1.8 2.4 2.5 2.5 1.4 0.4 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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