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NR5A2_HUMAN_295_540

Nuclear receptor subfamily 5 group A member 2 [Nuclear hormone receptor family. NR5 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NR5A2_HUMAN):D: NR LBD (341:343, 345, 346, 348, 349, 382, 383, 386, 387, 390, 403, 405, 411, 415:424, 427, 428, 431, 509, 513, 514, 516, 517, 519, 520, 525, 532, 536)
R: Lipid binding (419:424)
341:343, 345, 346, 348, 349, 382, 383, 386, 387, 390, 403, 405, 411, 415:424, 427, 428, 431, 509, 513, 514, 516, 517, 519, 520, 525, 532, 536

Full PDB list

1yok, 1yuc, 1zdu, 3plz, 3tx7, 4dor, 4dos, 4is8, 4oni, 4pld, 4ple, 4rwv, 5l11, 5syz, 5unj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
3
4
1
F
3
4
2
M
3
4
5
C
3
4
6
M
3
4
8
A
3
4
9
W
3
8
2
S
3
8
3
L
3
8
6
I
3
8
7
H
3
9
0
I
4
0
3
L
4
0
5
V
4
1
1
I
4
1
5
I
4
1
6
Q
4
1
9
A
4
2
0
G
4
2
1
A
4
2
2
T
4
2
3
L
4
2
4
L
4
2
7
M
4
2
8
A
4
3
1
A
5
1
3
E
5
1
4
Y
5
1
6
L
5
1
7
Y
5
1
9
K
5
2
0
L
5
3
2
[1]1zdu.a p3a58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dos.a plc41 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oni.b p6l51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ple.a eph47 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4rwv.a piz67 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5l11.a rjw29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5syz.a 71w29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3plz.b 47029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]4pld.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[4]4is8.a none . . . . . . . . . . . . . . . . H T E V A F . . . . . . . . . .

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
T
3
4
1
F
3
4
2
G
3
4
3
M
3
4
5
C
3
4
6
M
3
4
8
A
3
4
9
W
3
8
2
S
3
8
3
L
3
8
6
I
3
8
7
H
3
9
0
I
4
0
3
L
4
0
5
V
4
1
1
I
4
1
5
I
4
1
6
A
4
1
7
S
4
1
8
Q
4
1
9
A
4
2
0
G
4
2
1
A
4
2
2
T
4
2
3
L
4
2
4
L
4
2
7
M
4
2
8
A
4
3
1
I
5
0
9
A
5
1
3
E
5
1
4
Y
5
1
6
L
5
1
7
Y
5
1
9
K
5
2
0
D
5
2
5
L
5
3
2
L
5
3
6
[1]1zdu.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]4dos.a . . . . . . . . . . . . . . . . . . . * . . . * . * . . . . . . . . . . . .
[1]4oni.b . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . . . . . . . . .
[1]4ple.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]4rwv.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]5l11.a . . . . . . . . . * . . . . . . * . . * * . . . . . . . . . . . * . . . . .
[1]5syz.a . . . . . . . . . . . . . . . . . . . * * . . . . . . . . . . . . . . . . .
[2]3plz.b * * . * . . . . . . . . . . . * * . . * . . . . . . . . . . . . * . . . . .
[3]4pld.a . . . * . . . . . . . . . . . . * . . * * . . . . * . . . . . . . . . . . .
[4]4is8.a . . . * . . . . . . . . . . . . * . . H T E V A F . * . . . . . . . . . . .

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
1zdu.a:p3a
4dos.a:plc
4oni.b:p6l
4ple.a:eph
4rwv.a:piz
5l11.a:rjw
5syz.a:71w
3plz.b:470
4pld.a is apo
4is8.a is apo
[1] 1zdu.a
0.1
0.1 0.3 0.1 1.1 0 0 1.1 - -
[1] 4dos.a 1.5
0.1
1.5 0.4 3.0 0.6 0.3 1.3 - -
[1] 4oni.b 0.3 0.4
0.1
0.1 2.9 0.2 0 1.0 - -
[1] 4ple.a 0.2 0.4 0.3
0.1
0.8 0.1 0 1.6 - -
[1] 4rwv.a 1.0 0.1 1.2 0.7
0
0.6 0.3 1.6 - -
[1] 5l11.a 4.3 3.8 3.6 3.5 6.4
0
0 0.9 - -
[1] 5syz.a 4.4 4.1 3.7 3.4 6.6 0
0
1.0 - -
[2] 3plz.b 10 9.2 7.7 7.8 12 0.9 0.9
0
- -
[3] 4pld.a 8.5 8.1 8.4 7.3 10 1.9 1.3 2.7
-
-
[4] 4is8.a 8.2 5.8 6.0 6.8 10 1.4 1.3 2.1 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
1zdu.a
4dos.a
4oni.b
4ple.a
4rwv.a
5l11.a
5syz.a
3plz.b
4pld.a
4is8.a
[1] 1zdu.a
0
.13 .07 .04 .08 .22 .20 .39 .32 .31
[1] 4dos.a .13
0
.11 .12 .12 .24 .24 .39 .28 .34
[1] 4oni.b .07 .11
0
.09 .13 .16 .14 .35 .27 .26
[1] 4ple.a .04 .12 .09
0
.05 .22 .22 .40 .31 .32
[1] 4rwv.a .08 .12 .13 .05
0
.26 .25 .41 .33 .36
[1] 5l11.a .22 .24 .16 .22 .26
0
.04 .25 .25 .23
[1] 5syz.a .20 .24 .14 .22 .25 .04
0
.24 .25 .24
[2] 3plz.b .39 .39 .35 .40 .41 .25 .24
0
.32 .41
[3] 4pld.a .32 .28 .27 .31 .33 .25 .25 .32
0
.26
[4] 4is8.a .31 .34 .26 .32 .36 .23 .24 .41 .26
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
1zdu.a
4dos.a
4oni.b
4ple.a
4rwv.a
5l11.a
5syz.a
3plz.b
4pld.a
4is8.a
[1] 1zdu.a
0
0.8 0.8 0.6 1.0 1.2 1.2 1.4 1.5 1.1
[1] 4dos.a 0.8
0
1.0 0.9 1.3 1.4 1.4 1.8 1.6 1.2
[1] 4oni.b 0.8 1.0
0
0.7 1.2 1.2 1.2 1.6 1.4 1.1
[1] 4ple.a 0.6 0.9 0.7
0
0.8 1.3 1.3 1.4 1.6 1.2
[1] 4rwv.a 1.0 1.3 1.2 0.8
0
1.8 1.8 1.8 2.1 1.7
[1] 5l11.a 1.2 1.4 1.2 1.3 1.8
0
0.1 1.2 1.1 0.8
[1] 5syz.a 1.2 1.4 1.2 1.3 1.8 0.1
0
1.2 1.1 0.8
[2] 3plz.b 1.4 1.8 1.6 1.4 1.8 1.2 1.2
0
1.9 1.4
[3] 4pld.a 1.5 1.6 1.4 1.6 2.1 1.1 1.1 1.9
0
1.1
[4] 4is8.a 1.1 1.2 1.1 1.2 1.7 0.8 0.8 1.4 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
1zdu.a
4dos.a
4oni.b
4ple.a
4rwv.a
5l11.a
5syz.a
3plz.b
4pld.a
4is8.a
[1] 1zdu.a
0
1.1 1.0 1.4 1.5 1.4 1.4 1.6 1.9 1.3
[1] 4dos.a 1.1
0
1.2 1.5 1.7 1.6 1.6 1.9 1.9 1.4
[1] 4oni.b 1.0 1.2
0
1.3 1.5 1.3 1.3 1.7 1.8 1.3
[1] 4ple.a 1.4 1.5 1.3
0
1.0 1.7 1.7 1.9 1.7 1.8
[1] 4rwv.a 1.5 1.7 1.5 1.0
0
2.0 2.0 2.2 2.1 2.0
[1] 5l11.a 1.4 1.6 1.3 1.7 2.0
0
0.3 1.3 1.7 1.2
[1] 5syz.a 1.4 1.6 1.3 1.7 2.0 0.3
0
1.3 1.7 1.2
[2] 3plz.b 1.6 1.9 1.7 1.9 2.2 1.3 1.3
0
2.3 1.6
[3] 4pld.a 1.9 1.9 1.8 1.7 2.1 1.7 1.7 2.3
0
1.7
[4] 4is8.a 1.3 1.4 1.3 1.8 2.0 1.2 1.2 1.6 1.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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