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VDRA_DANRE_155_453_ligBind

Vitamin D3 receptor A [Nuclear hormone receptor family. NR1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (VDRA_DANRE):D: NR LBD (175, 179, 182, 255, 258, 259, 261, 262, 264, 265, 296, 299, 300, 302, 303, 306, 314, 316, 323, 328, 331, 333, 334, 337, 338, 341, 419, 422, 423, 426, 427, 430, 436, 440, 444, 448)
R: Vitamin D3 binding (255, 258, 259, 261, 262, 264, 265)
R: Vitamin D3 binding (299, 300, 302, 303, 306)
175, 179, 182, 255, 258, 259, 261, 262, 264, 265, 296, 299, 300, 302, 303, 306, 314, 316, 323, 328, 331, 333, 334, 337, 338, 341, 419, 422, 423, 426, 427, 430, 436, 440, 444, 448

Full PDB list

2hbh, 2hc4, 2hcd, 3dr1, 3o1d, 3o1e, 4fhh, 4fhi, 4g1d, 4g1y, 4g1z, 4g20, 4g21, 4g2h, 4ia1, 4ia2, 4ia3, 4ia7, 4q0a, 4ruj, 4ruo, 4rup, 5e7v, 5lga, 5mx7, 5nky, 5nma, 5nmb (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
7
5
Y
1
7
9
F
1
8
2
L
2
5
5
L
2
5
8
A
2
5
9
L
2
6
1
V
2
6
2
Y
2
6
4
S
2
6
5
I
2
9
6
I
2
9
9
M
3
0
0
R
3
0
2
S
3
0
3
S
3
0
6
W
3
1
4
C
3
1
6
Y
3
2
3
V
3
2
8
A
3
3
1
H
3
3
3
L
3
3
7
L
3
3
8
L
3
4
1
L
4
1
9
H
4
2
3
Y
4
2
7
L
4
3
0
L
4
4
0
V
4
4
4
F
4
4
8
[1]2hbh.a xe429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2hc4.a vdx30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3dr1.a c5d33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3o1d.a g7241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3o1e.a h9741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4fhh.a 0u333 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4fhi.a 0s433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4g1d.a 0vk34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4g1y.a 0vo30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4g1z.a 0vp35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4g20.a 48434 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4g2h.a 0vq34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ia1.a biv35 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4q0a.c 4oa27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ruj.a vdx30 . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . .
[1]4ruo.x biv36 . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . .
[1]4rup.a h9741 . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . .
[1]5e7v.a m7e38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lga.a 6vh42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5mx7.1 d3v30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nky.a 91w32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nma.a 9cw32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nmb.2 9cz32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
7
5
Y
1
7
9
F
1
8
2
L
2
5
5
L
2
5
8
A
2
5
9
L
2
6
1
V
2
6
2
Y
2
6
4
S
2
6
5
I
2
9
6
I
2
9
9
M
3
0
0
R
3
0
2
S
3
0
3
S
3
0
6
W
3
1
4
C
3
1
6
Y
3
2
3
V
3
2
8
A
3
3
1
H
3
3
3
T
3
3
4
L
3
3
7
L
3
3
8
L
3
4
1
L
4
1
9
E
4
2
2
H
4
2
3
Q
4
2
6
Y
4
2
7
L
4
3
0
H
4
3
6
L
4
4
0
V
4
4
4
F
4
4
8
[1]2hbh.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]2hc4.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]3dr1.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]3o1d.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]3o1e.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4fhh.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]4fhi.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]4g1d.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4g1y.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]4g1z.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4g20.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4g2h.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]4ia1.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]4q0a.c . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4ruj.a . . . . . . . . . . . . . . . . . . . * . . . H . . . . . . . . . . . .
[1]4ruo.x . . . . . . . . . . . . . . . . . . . * . . . H . . . . . . . . . . . .
[1]4rup.a . . . . . . . . . . . . . . . . . . . * . . . H . . . . . . . . . . . .
[1]5e7v.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]5lga.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]5mx7.1 . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]5nky.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]5nma.a . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .
[1]5nmb.2 . . . . . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . .

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
2hbh.a:xe4
2hc4.a:vdx
3dr1.a:c5d
3o1d.a:g72
3o1e.a:h97
4fhh.a:0u3
4fhi.a:0s4
4g1d.a:0vk
4g1y.a:0vo
4g1z.a:0vp
4g20.a:484
4g2h.a:0vq
4ia1.a:biv
4q0a.c:4oa
4ruj.a:vdx
4ruo.x:biv
4rup.a:h97
5e7v.a:m7e
5lga.a:6vh
5mx7.1:d3v
5nky.a:91w
5nma.a:9cw
5nmb.2:9cz
[1] 2hbh.a
0
0.1 0 2.3 2.2 0.5 0.6 0.9 0.5 1.6 1.0 0 2.5 0.5 0 2.1 1.9 0.2 2.4 0.1 0.1 0.1 0.1
[1] 2hc4.a 0
0
0 2.2 1.9 0.3 0.5 0.9 0.4 1.7 0.8 0 2.4 0.6 0 2.1 1.8 0.3 2.2 0 0.1 0 0
[1] 3dr1.a 0 0
0
2.3 2.0 0.3 0.8 0.6 0.3 1.5 0.6 0 2.0 0.5 0 2.1 1.8 0.1 2.5 0 0.1 0 0.1
[1] 3o1d.a 0 0 0
0
0.1 0.4 0.6 0.4 0.3 1.3 0.7 0 0.1 0.4 0 0 0 0.1 0.2 0 0 0 0
[1] 3o1e.a 0.1 0.1 0.3 0.1
0
0.4 0.6 0.5 0.4 0.7 0.5 0.1 0.1 0.4 0 0.1 0.1 0 0.1 0 0 0.1 0.1
[1] 4fhh.a 0.1 0 0.1 2.2 1.9
0.2
0.3 0.7 0.1 1.4 0.7 0 2.2 0.5 0 1.8 1.5 0.1 2.2 0 0 0 0
[1] 4fhi.a 0.1 0 0.1 2.2 1.9 0.3
0.2
0.8 0 1.5 0.8 0 2.3 0.5 0 1.8 1.7 0 2.2 0 0 0 0
[1] 4g1d.a 0 0 0.1 2.1 2.0 0.3 0.4
0
0 0.1 0 0.1 2.2 0.3 0 2.1 1.8 0.1 2.4 0 0.1 0 0.1
[1] 4g1y.a 0.1 0 0.1 1.8 1.9 0.3 0.6 0.6
0
1.3 0.7 0 2.2 0.6 0 1.9 1.5 0.1 2.2 0 0 0 0.1
[1] 4g1z.a 0 0.1 0.2 2.3 2.1 0.4 0.5 0.1 0.2
0.1
0.1 0.2 2.2 0.1 0 2.1 1.8 0.1 2.7 0 0.1 0.1 0.1
[1] 4g20.a 0 0 0.1 2.3 2.5 0.4 0.4 0.1 0 0.4
0
0.2 2.3 0.4 0 2.2 2.1 0.1 2.8 0 0.1 0 0.1
[1] 4g2h.a 0 0 0.1 1.9 1.8 0.8 1.0 1.2 0.2 1.9 0.8
0
2.4 0.5 0 1.9 1.2 0.1 2.0 0 0.1 0.3 0.4
[1] 4ia1.a 0 0 0 0 0 0.4 0.6 0.7 0.2 1.6 0.8 0
0
0.4 0 0.1 0 0.1 0.1 0 0 0 0
[1] 4q0a.c 0.3 0.3 0.3 2.7 2.7 0.4 0.5 0.8 0.9 0.6 0.6 0.2 3.0
0.1
0.2 2.6 2.2 0.5 3.4 0.3 0.2 0.2 0.3
[1] 4ruj.a 0 0 0.2 2.7 2.5 0.5 0.5 0.7 0.6 1.6 0.7 0 2.7 0.6
0
2.3 2.2 0.2 3.0 0 0 0 0
[1] 4ruo.x 0 0.1 0.1 0 0 0.4 0.7 0.7 0.1 1.6 0.6 0.1 0 0.6 0
0
0 0 0 0 0 0 0
[1] 4rup.a 0 0 0.1 0 0 0.5 0.7 0.6 0.4 1.6 0.8 0.1 0.1 0.6 0.1 0.1
0
0.2 0 0 0 0 0
[1] 5e7v.a 0 0 0.1 2.1 1.8 0.4 0.5 0.6 0.3 1.3 0.6 0.1 2.4 0.7 0 2.0 2.0
0
2.2 0 0 0 0.1
[1] 5lga.a 0 0 0.1 0 0.1 0.4 0.4 0.5 0.5 0.9 0.7 0.1 0.1 0.4 0 0.1 0 0.1
0
0 0 0 0
[1] 5mx7.1 0 0 0.4 2.3 2.0 0.6 0.6 0.8 0.3 1.3 0.8 0.2 2.3 0.7 0 2.0 1.7 0.3 2.5
0
0 0 0.2
[1] 5nky.a 0 0 0.2 2.2 2.1 0.5 0.5 0.6 0.3 1.2 0.8 0.1 2.3 0.7 0 2.1 1.7 0.3 2.3 0
0
0 0
[1] 5nma.a 0 0 0.1 2.2 2.1 0.6 0.7 0.6 0.3 1.4 0.6 0 2.1 0.5 0 2.1 1.6 0.1 2.3 0 0
0
0
[1] 5nmb.2 0 0 0.1 2.4 2.4 0.3 0.5 0.7 0.6 1.7 0.8 0.2 2.3 0.7 0 2.3 1.9 0.3 2.4 0 0 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
2hbh.a
2hc4.a
3dr1.a
3o1d.a
3o1e.a
4fhh.a
4fhi.a
4g1d.a
4g1y.a
4g1z.a
4g20.a
4g2h.a
4ia1.a
4q0a.c
4ruj.a
4ruo.x
4rup.a
5e7v.a
5lga.a
5mx7.1
5nky.a
5nma.a
5nmb.2
[1] 2hbh.a
0
.04 .02 .09 .11 .04 .03 .08 .03 .08 .07 .03 .09 .10 .04 .09 .08 .03 .11 .04 .05 .04 .03
[1] 2hc4.a .04
0
.03 .10 .11 .04 .04 .08 .04 .09 .08 .06 .09 .09 .04 .10 .09 .04 .10 .03 .03 .03 .02
[1] 3dr1.a .02 .03
0
.08 .12 .04 .03 .08 .03 .07 .07 .05 .10 .11 .05 .10 .09 .03 .10 .05 .04 .04 .04
[1] 3o1d.a .09 .10 .08
0
.04 .09 .09 .12 .09 .12 .12 .10 .04 .14 .12 .03 .03 .09 .03 .11 .10 .09 .10
[1] 3o1e.a .11 .11 .12 .04
0
.11 .11 .11 .11 .11 .11 .13 .05 .13 .12 .04 .04 .11 .02 .10 .11 .10 .11
[1] 4fhh.a .04 .04 .04 .09 .11
0
.01 .07 .03 .08 .06 .04 .09 .10 .05 .09 .08 .04 .10 .06 .05 .04 .06
[1] 4fhi.a .03 .04 .03 .09 .11 .01
0
.06 .02 .08 .06 .04 .09 .10 .05 .09 .09 .04 .09 .06 .05 .04 .06
[1] 4g1d.a .08 .08 .08 .12 .11 .07 .06
0
.08 .03 .03 .09 .14 .06 .08 .13 .14 .06 .10 .06 .06 .06 .08
[1] 4g1y.a .03 .04 .03 .09 .11 .03 .02 .08
0
.08 .07 .04 .08 .10 .06 .09 .09 .04 .10 .05 .05 .04 .05
[1] 4g1z.a .08 .09 .07 .12 .11 .08 .08 .03 .08
0
.03 .09 .14 .06 .08 .14 .14 .07 .11 .06 .06 .07 .08
[1] 4g20.a .07 .08 .07 .12 .11 .06 .06 .03 .07 .03
0
.09 .14 .06 .07 .14 .14 .06 .11 .05 .06 .06 .07
[1] 4g2h.a .03 .06 .05 .10 .13 .04 .04 .09 .04 .09 .09
0
.11 .11 .06 .10 .10 .04 .12 .06 .06 .04 .06
[1] 4ia1.a .09 .09 .10 .04 .05 .09 .09 .14 .08 .14 .14 .11
0
.16 .11 .02 .03 .10 .05 .10 .10 .09 .11
[1] 4q0a.c .10 .09 .11 .14 .13 .10 .10 .06 .10 .06 .06 .11 .16
0
.09 .17 .16 .09 .14 .08 .09 .09 .09
[1] 4ruj.a .04 .04 .05 .12 .12 .05 .05 .08 .06 .08 .07 .06 .11 .09
0
.11 .10 .04 .11 .05 .04 .05 .05
[1] 4ruo.x .09 .10 .10 .03 .04 .09 .09 .13 .09 .14 .14 .10 .02 .17 .11
0
.03 .10 .04 .11 .11 .09 .11
[1] 4rup.a .08 .09 .09 .03 .04 .08 .09 .14 .09 .14 .14 .10 .03 .16 .10 .03
0
.09 .04 .10 .10 .09 .09
[1] 5e7v.a .03 .04 .03 .09 .11 .04 .04 .06 .04 .07 .06 .04 .10 .09 .04 .10 .09
0
.10 .05 .03 .04 .05
[1] 5lga.a .11 .10 .10 .03 .02 .10 .09 .10 .10 .11 .11 .12 .05 .14 .11 .04 .04 .10
0
.09 .10 .10 .10
[1] 5mx7.1 .04 .03 .05 .11 .10 .06 .06 .06 .05 .06 .05 .06 .10 .08 .05 .11 .10 .05 .09
0
.02 .04 .03
[1] 5nky.a .05 .03 .04 .10 .11 .05 .05 .06 .05 .06 .06 .06 .10 .09 .04 .11 .10 .03 .10 .02
0
.03 .03
[1] 5nma.a .04 .03 .04 .09 .10 .04 .04 .06 .04 .07 .06 .04 .09 .09 .05 .09 .09 .04 .10 .04 .03
0
.03
[1] 5nmb.2 .03 .02 .04 .10 .11 .06 .06 .08 .05 .08 .07 .06 .11 .09 .05 .11 .09 .05 .10 .03 .03 .03
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

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
2hbh.a
2hc4.a
3dr1.a
3o1d.a
3o1e.a
4fhh.a
4fhi.a
4g1d.a
4g1y.a
4g1z.a
4g20.a
4g2h.a
4ia1.a
4q0a.c
4ruj.a
4ruo.x
4rup.a
5e7v.a
5lga.a
5mx7.1
5nky.a
5nma.a
5nmb.2
[1] 2hbh.a
0
0.2 0.2 0.5 0.6 0.3 0.3 0.5 0.2 0.5 0.4 0.2 0.5 0.5 0.3 0.5 0.4 0.3 0.6 0.3 0.3 0.3 0.3
[1] 2hc4.a 0.2
0
0.2 0.5 0.5 0.2 0.3 0.4 0.2 0.5 0.4 0.2 0.4 0.5 0.3 0.4 0.4 0.3 0.5 0.3 0.2 0.3 0.2
[1] 3dr1.a 0.2 0.2
0
0.5 0.6 0.3 0.3 0.5 0.2 0.5 0.3 0.2 0.4 0.5 0.3 0.5 0.4 0.3 0.6 0.3 0.3 0.3 0.3
[1] 3o1d.a 0.5 0.5 0.5
0
0.3 0.5 0.5 0.6 0.5 0.6 0.6 0.5 0.2 0.7 0.3 0.3 0.3 0.5 0.2 0.5 0.5 0.5 0.5
[1] 3o1e.a 0.6 0.5 0.6 0.3
0
0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.3 0.7 0.4 0.4 0.4 0.6 0.3 0.5 0.6 0.6 0.5
[1] 4fhh.a 0.3 0.2 0.3 0.5 0.6
0
0.1 0.4 0.2 0.5 0.4 0.2 0.5 0.5 0.3 0.5 0.4 0.2 0.6 0.3 0.3 0.3 0.3
[1] 4fhi.a 0.3 0.3 0.3 0.5 0.6 0.1
0
0.5 0.3 0.5 0.4 0.3 0.5 0.5 0.4 0.5 0.4 0.3 0.6 0.3 0.3 0.4 0.3
[1] 4g1d.a 0.5 0.4 0.5 0.6 0.6 0.4 0.5
0
0.4 0.3 0.3 0.4 0.6 0.4 0.5 0.6 0.6 0.5 0.6 0.4 0.4 0.4 0.3
[1] 4g1y.a 0.2 0.2 0.2 0.5 0.6 0.2 0.3 0.4
0
0.5 0.4 0.2 0.4 0.5 0.3 0.5 0.4 0.3 0.6 0.3 0.3 0.3 0.3
[1] 4g1z.a 0.5 0.5 0.5 0.6 0.6 0.5 0.5 0.3 0.5
0
0.2 0.5 0.6 0.4 0.6 0.6 0.6 0.5 0.6 0.4 0.4 0.5 0.4
[1] 4g20.a 0.4 0.4 0.3 0.6 0.6 0.4 0.4 0.3 0.4 0.2
0
0.3 0.6 0.4 0.5 0.6 0.5 0.4 0.6 0.3 0.3 0.4 0.3
[1] 4g2h.a 0.2 0.2 0.2 0.5 0.6 0.2 0.3 0.4 0.2 0.5 0.3
0
0.4 0.5 0.3 0.5 0.4 0.3 0.6 0.3 0.3 0.3 0.3
[1] 4ia1.a 0.5 0.4 0.4 0.2 0.3 0.5 0.5 0.6 0.4 0.6 0.6 0.4
0
0.7 0.3 0.3 0.2 0.5 0.3 0.5 0.5 0.5 0.5
[1] 4q0a.c 0.5 0.5 0.5 0.7 0.7 0.5 0.5 0.4 0.5 0.4 0.4 0.5 0.7
0
0.6 0.7 0.7 0.5 0.7 0.5 0.5 0.6 0.5
[1] 4ruj.a 0.3 0.3 0.3 0.3 0.4 0.3 0.4 0.5 0.3 0.6 0.5 0.3 0.3 0.6
0
0.3 0.3 0.3 0.4 0.3 0.3 0.4 0.3
[1] 4ruo.x 0.5 0.4 0.5 0.3 0.4 0.5 0.5 0.6 0.5 0.6 0.6 0.5 0.3 0.7 0.3
0
0.3 0.5 0.3 0.5 0.5 0.5 0.5
[1] 4rup.a 0.4 0.4 0.4 0.3 0.4 0.4 0.4 0.6 0.4 0.6 0.5 0.4 0.2 0.7 0.3 0.3
0
0.4 0.4 0.4 0.4 0.5 0.4
[1] 5e7v.a 0.3 0.3 0.3 0.5 0.6 0.2 0.3 0.5 0.3 0.5 0.4 0.3 0.5 0.5 0.3 0.5 0.4
0
0.6 0.2 0.2 0.3 0.3
[1] 5lga.a 0.6 0.5 0.6 0.2 0.3 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.3 0.7 0.4 0.3 0.4 0.6
0
0.5 0.5 0.6 0.5
[1] 5mx7.1 0.3 0.3 0.3 0.5 0.5 0.3 0.3 0.4 0.3 0.4 0.3 0.3 0.5 0.5 0.3 0.5 0.4 0.2 0.5
0
0.2 0.3 0.2
[1] 5nky.a 0.3 0.2 0.3 0.5 0.6 0.3 0.3 0.4 0.3 0.4 0.3 0.3 0.5 0.5 0.3 0.5 0.4 0.2 0.5 0.2
0
0.3 0.2
[1] 5nma.a 0.3 0.3 0.3 0.5 0.6 0.3 0.4 0.4 0.3 0.5 0.4 0.3 0.5 0.6 0.4 0.5 0.5 0.3 0.6 0.3 0.3
0
0.3
[1] 5nmb.2 0.3 0.2 0.3 0.5 0.5 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.5 0.5 0.3 0.5 0.4 0.3 0.5 0.2 0.2 0.3
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
2hbh.a
2hc4.a
3dr1.a
3o1d.a
3o1e.a
4fhh.a
4fhi.a
4g1d.a
4g1y.a
4g1z.a
4g20.a
4g2h.a
4ia1.a
4q0a.c
4ruj.a
4ruo.x
4rup.a
5e7v.a
5lga.a
5mx7.1
5nky.a
5nma.a
5nmb.2
[1] 2hbh.a
0
0.2 0.3 0.7 0.8 0.4 0.4 0.5 0.3 0.6 0.5 0.3 0.7 1.0 0.6 0.9 0.8 0.4 0.8 0.7 0.6 0.7 0.7
[1] 2hc4.a 0.2
0
0.3 0.7 0.8 0.3 0.4 0.5 0.3 0.6 0.5 0.3 0.7 1.1 0.6 0.9 0.8 0.4 0.8 0.7 0.6 0.7 0.7
[1] 3dr1.a 0.3 0.3
0
0.7 0.8 0.4 0.4 0.6 0.4 0.6 0.5 0.4 0.7 1.1 0.6 0.9 0.8 0.4 0.8 0.7 0.6 0.7 0.6
[1] 3o1d.a 0.7 0.7 0.7
0
0.4 0.7 0.7 0.8 0.7 0.9 0.8 0.8 0.5 1.2 0.5 0.6 0.4 0.7 0.5 0.8 0.8 0.9 0.8
[1] 3o1e.a 0.8 0.8 0.8 0.4
0
0.8 0.8 0.8 0.8 0.8 0.9 0.8 0.6 1.2 0.7 0.7 0.5 0.8 0.6 0.9 0.9 0.9 0.9
[1] 4fhh.a 0.4 0.3 0.4 0.7 0.8
0
0.3 0.5 0.3 0.6 0.5 0.4 0.7 1.1 0.6 0.9 0.8 0.3 0.8 0.7 0.6 0.8 0.7
[1] 4fhi.a 0.4 0.4 0.4 0.7 0.8 0.3
0
0.6 0.4 0.6 0.5 0.4 0.7 1.1 0.6 0.9 0.8 0.4 0.8 0.7 0.6 0.8 0.7
[1] 4g1d.a 0.5 0.5 0.6 0.8 0.8 0.5 0.6
0
0.6 0.4 0.3 0.6 0.8 1.0 0.7 1.0 0.9 0.6 0.9 0.8 0.7 0.8 0.7
[1] 4g1y.a 0.3 0.3 0.4 0.7 0.8 0.3 0.4 0.6
0
0.6 0.5 0.3 0.7 1.1 0.6 0.9 0.8 0.4 0.8 0.7 0.6 0.7 0.7
[1] 4g1z.a 0.6 0.6 0.6 0.9 0.8 0.6 0.6 0.4 0.6
0
0.4 0.6 0.9 1.0 0.8 1.0 0.9 0.6 0.9 0.8 0.7 0.9 0.8
[1] 4g20.a 0.5 0.5 0.5 0.8 0.9 0.5 0.5 0.3 0.5 0.4
0
0.5 0.8 1.0 0.7 1.0 0.9 0.6 0.9 0.8 0.7 0.8 0.7
[1] 4g2h.a 0.3 0.3 0.4 0.8 0.8 0.4 0.4 0.6 0.3 0.6 0.5
0
0.7 1.1 0.6 0.9 0.8 0.4 0.8 0.7 0.6 0.8 0.7
[1] 4ia1.a 0.7 0.7 0.7 0.5 0.6 0.7 0.7 0.8 0.7 0.9 0.8 0.7
0
1.2 0.7 0.7 0.6 0.7 0.7 0.9 0.8 0.9 0.9
[1] 4q0a.c 1.0 1.1 1.1 1.2 1.2 1.1 1.1 1.0 1.1 1.0 1.0 1.1 1.2
0
1.1 1.3 1.2 1.1 1.1 1.0 0.9 1.0 0.9
[1] 4ruj.a 0.6 0.6 0.6 0.5 0.7 0.6 0.6 0.7 0.6 0.8 0.7 0.6 0.7 1.1
0
1.0 0.9 0.6 0.6 0.7 0.6 0.7 0.6
[1] 4ruo.x 0.9 0.9 0.9 0.6 0.7 0.9 0.9 1.0 0.9 1.0 1.0 0.9 0.7 1.3 1.0
0
0.6 0.9 0.6 0.9 0.9 1.0 1.0
[1] 4rup.a 0.8 0.8 0.8 0.4 0.5 0.8 0.8 0.9 0.8 0.9 0.9 0.8 0.6 1.2 0.9 0.6
0
0.8 0.6 0.9 0.9 1.0 0.9
[1] 5e7v.a 0.4 0.4 0.4 0.7 0.8 0.3 0.4 0.6 0.4 0.6 0.6 0.4 0.7 1.1 0.6 0.9 0.8
0
0.8 0.7 0.6 0.7 0.7
[1] 5lga.a 0.8 0.8 0.8 0.5 0.6 0.8 0.8 0.9 0.8 0.9 0.9 0.8 0.7 1.1 0.6 0.6 0.6 0.8
0
0.8 0.8 0.9 0.8
[1] 5mx7.1 0.7 0.7 0.7 0.8 0.9 0.7 0.7 0.8 0.7 0.8 0.8 0.7 0.9 1.0 0.7 0.9 0.9 0.7 0.8
0
0.4 0.6 0.5
[1] 5nky.a 0.6 0.6 0.6 0.8 0.9 0.6 0.6 0.7 0.6 0.7 0.7 0.6 0.8 0.9 0.6 0.9 0.9 0.6 0.8 0.4
0
0.5 0.4
[1] 5nma.a 0.7 0.7 0.7 0.9 0.9 0.8 0.8 0.8 0.7 0.9 0.8 0.8 0.9 1.0 0.7 1.0 1.0 0.7 0.9 0.6 0.5
0
0.5
[1] 5nmb.2 0.7 0.7 0.6 0.8 0.9 0.7 0.7 0.7 0.7 0.8 0.7 0.7 0.9 0.9 0.6 1.0 0.9 0.7 0.8 0.5 0.4 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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