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STF1_HUMAN_220_461_ligBind

Steroidogenic factor 1 [Nuclear hormone receptor family. NR5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (STF1_HUMAN):D: NR LBD (260:262, 265, 266, 268, 269, 302, 303, 306, 307, 310, 323, 325, 331, 335, 336, 339:342, 344, 347, 348, 351, 429, 430, 433, 434, 436, 437, 439, 440, 452)
R: Important for dimerization (260:262, 265, 266, 268, 269, 302, 303, 306, 307, 310, 323, 325, 331, 335, 336, 339:342, 344, 347, 348, 351, 429, 430, 433, 434, 436, 437, 439, 440, 452)
260:262, 265, 266, 268, 269, 302, 303, 306, 307, 310, 323, 325, 331, 335, 336, 339:342, 344, 347, 348, 351, 429, 430, 433, 434, 436, 437, 439, 440, 452

Full PDB list

1ymt, 1yow, 1yp0, 1zdt, 3f7d, 4qjr, 4qk4

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
2
6
0
A
2
6
1
F
2
6
2
L
2
6
5
C
2
6
6
M
2
6
8
A
2
6
9
W
3
0
2
S
3
0
3
L
3
0
6
V
3
0
7
H
3
1
0
I
3
2
3
L
3
2
5
V
3
3
1
V
3
3
6
Q
3
3
9
A
3
4
0
G
3
4
1
L
3
4
4
L
3
4
7
V
3
4
8
A
3
5
1
L
4
2
9
S
4
3
0
A
4
3
3
Y
4
3
6
L
4
3
7
H
4
3
9
K
4
4
0
L
4
5
2
[1]1ymt.a dr951 . P . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yow.a p0e46 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yp0.a pef47 . P . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zdt.a pef47 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3f7d.a p4252 . P . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qjr.a piz67 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qk4.a pik63 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
A
2
6
0
A
2
6
1
F
2
6
2
L
2
6
5
C
2
6
6
M
2
6
8
A
2
6
9
W
3
0
2
S
3
0
3
L
3
0
6
V
3
0
7
H
3
1
0
I
3
2
3
L
3
2
5
V
3
3
1
T
3
3
5
V
3
3
6
Q
3
3
9
A
3
4
0
G
3
4
1
S
3
4
2
L
3
4
4
L
3
4
7
V
3
4
8
A
3
5
1
L
4
2
9
S
4
3
0
A
4
3
3
K
4
3
4
Y
4
3
6
L
4
3
7
H
4
3
9
K
4
4
0
L
4
5
2
[1]1ymt.a . P . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yow.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yp0.a . P . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zdt.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3f7d.a . P . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qjr.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qk4.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
1ymt.a:dr9
1yow.a:p0e
1yp0.a:pef
1zdt.a:pef
3f7d.a:p42
4qjr.a:piz
4qk4.a:pik
[1] 1ymt.a
0
0.4 0 0 0.1 0.3 0.2
[1] 1yow.a 0.2
0.1
0 0.1 0.3 0.2 0
[1] 1yp0.a 0.1 0.4
0
0 0.5 0.5 0.3
[1] 1zdt.a 0 0.5 0.1
0
0.2 0.3 0.3
[1] 3f7d.a 0.3 0.6 0.2 0.2
0
0.3 0.3
[1] 4qjr.a 0.5 0.6 0.4 0.4 0.6
0.1
0.1
[1] 4qk4.a 0.3 0.3 0.2 0.2 0.4 0.1
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
1ymt.a
1yow.a
1yp0.a
1zdt.a
3f7d.a
4qjr.a
4qk4.a
[1] 1ymt.a
0
.02 .01 .01 .03 .04 .03
[1] 1yow.a .02
0
.02 .02 .03 .03 .02
[1] 1yp0.a .01 .02
0
.01 .04 .04 .04
[1] 1zdt.a .01 .02 .01
0
.03 .04 .03
[1] 3f7d.a .03 .03 .04 .03
0
.04 .03
[1] 4qjr.a .04 .03 .04 .04 .04
0
.01
[1] 4qk4.a .03 .02 .04 .03 .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1ymt.a
1yow.a
1yp0.a
1zdt.a
3f7d.a
4qjr.a
4qk4.a
[1] 1ymt.a
0
1.2 0.3 0.3 1.1 1.2 1.2
[1] 1yow.a 1.2
0
1.1 1.2 0.9 0.4 0.4
[1] 1yp0.a 0.3 1.1
0
0.4 1.1 1.1 1.1
[1] 1zdt.a 0.3 1.2 0.4
0
1.1 1.2 1.2
[1] 3f7d.a 1.1 0.9 1.1 1.1
0
0.9 1.0
[1] 4qjr.a 1.2 0.4 1.1 1.2 0.9
0
0.2
[1] 4qk4.a 1.2 0.4 1.1 1.2 1.0 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1ymt.a
1yow.a
1yp0.a
1zdt.a
3f7d.a
4qjr.a
4qk4.a
[1] 1ymt.a
0
1.2 0.7 0.7 1.3 1.3 1.3
[1] 1yow.a 1.2
0
1.3 1.3 1.2 0.7 0.7
[1] 1yp0.a 0.7 1.3
0
0.7 1.4 1.3 1.3
[1] 1zdt.a 0.7 1.3 0.7
0
1.4 1.3 1.3
[1] 3f7d.a 1.3 1.2 1.4 1.4
0
1.3 1.3
[1] 4qjr.a 1.3 0.7 1.3 1.3 1.3
0
0.3
[1] 4qk4.a 1.3 0.7 1.3 1.3 1.3 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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