If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

EPAS1_HUMAN_238_353

Endothelial PAS domain-containing protein 1

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPAS1_HUMAN):D: PAS 2 (244, 246, 248, 252, 254, 261, 277, 280, 281, 289, 292, 293, 296)
D: PAC (304, 307, 309, 319, 321, 337, 339, 341)
302
244, 246, 248, 252, 254, 261, 277, 280, 281, 289, 292, 293, 296, 302, 304, 307, 309, 319, 321, 337, 339, 341

Full PDB list

3f1n, 3f1o, 3f1p, 3h7w, 3h82, 4ghi, 4gs9, 4pky, 4zp4, 4zph, 4zqd, 5tbm, 5ufp (redundant Pocketome entry); 4xt2 (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
2
4
4
S
2
4
6
H
2
4
8
M
2
5
2
F
2
5
4
A
2
7
7
F
2
8
0
Y
2
8
1
M
2
8
9
S
2
9
2
H
2
9
3
L
2
9
6
V
3
0
2
S
3
0
4
Y
3
0
7
M
3
0
9
L
3
1
9
T
3
2
1
I
3
3
7
C
3
3
9
N
3
4
1
[1]3f1n.a none . . . . . . . . . . . . . . . . . . . . .
[1]3f1o.a 2xy20 . . . . . . . . . . . . . . . . . . . . .
[1]3h7w.a 01820 . . . . . . . . . . . . . . . . . . . . .
[1]3h82.a 02020 . . . . . . . . . . . . . . . . . . . . .
[1]4ghi.a 0x321 . . . . . . . . . . . . . . . . . . . . .
[1]4gs9.a 0xb20 . . . . . . . . . . . . . . . . . . . . .
[1]5tbm.a 79a26 . . . . . . . . . . . . . . . . . . . . .
[1]5ufp.a 86d28 . . . . . . . . . . . . . . . . . . . . .

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
2
4
4
S
2
4
6
H
2
4
8
M
2
5
2
F
2
5
4
I
2
6
1
A
2
7
7
F
2
8
0
Y
2
8
1
M
2
8
9
S
2
9
2
H
2
9
3
L
2
9
6
V
3
0
2
S
3
0
4
Y
3
0
7
M
3
0
9
L
3
1
9
T
3
2
1
I
3
3
7
C
3
3
9
N
3
4
1
[1]3f1n.a . . . * . . . . . . . . . . . . . . . . . .
[1]3f1o.a . . . . . . . . . . . . . . . . . . . . . .
[1]3h7w.a . . . . . . . . . . . . . . . . . . . . . .
[1]3h82.a . . . . . . . . . . . . . . . . . . . . . .
[1]4ghi.a . . . . . . . . . . . . . . . . . . . . . .
[1]4gs9.a . . . * . . . . . . . . . . . . . . . . . .
[1]5tbm.a . . . . . . . . . . . . . . . . . . . . . .
[1]5ufp.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
3f1n.a is apo
3f1o.a:2xy
3h7w.a:018
3h82.a:020
4ghi.a:0x3
4gs9.a:0xb
5tbm.a:79a
5ufp.a:86d
[1] 3f1n.a
-
1.3 1.9 1.5 0.8 1.5 2.3 2.3
[1] 3f1o.a -
0
0.2 0.1 0.1 0.1 1.4 1.6
[1] 3h7w.a - 0.1
0.3
0.1 0.2 0.2 0.7 0.9
[1] 3h82.a - 0 0.1
0
0.4 0 0.6 0.8
[1] 4ghi.a - 0.2 0.3 0.2
0
0 0.5 0.6
[1] 4gs9.a - 1.5 1.6 1.6 0.9
1.3
2.1 2.3
[1] 5tbm.a - 0.1 0 0.2 0.1 0.1
0
0.2
[1] 5ufp.a - 0 0.1 0.1 0.1 0.1 0
0.1
[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
3f1n.a
3f1o.a
3h7w.a
3h82.a
4ghi.a
4gs9.a
5tbm.a
5ufp.a
[1] 3f1n.a
0
.12 .06 .10 .09 .01 .10 .12
[1] 3f1o.a .12
0
.07 .07 .07 .13 .07 .07
[1] 3h7w.a .06 .07
0
.03 .03 .07 .04 .06
[1] 3h82.a .10 .07 .03
0
.05 .10 .04 .05
[1] 4ghi.a .09 .07 .03 .05
0
.08 .03 .04
[1] 4gs9.a .01 .13 .07 .10 .08
0
.11 .13
[1] 5tbm.a .10 .07 .04 .04 .03 .11
0
.02
[1] 5ufp.a .12 .07 .06 .05 .04 .13 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3f1n.a
3f1o.a
3h7w.a
3h82.a
4ghi.a
4gs9.a
5tbm.a
5ufp.a
[1] 3f1n.a
0
0.2 0.4 0.5 0.3 0.2 0.3 0.4
[1] 3f1o.a 0.2
0
0.4 0.5 0.3 0.3 0.3 0.3
[1] 3h7w.a 0.4 0.4
0
0.3 0.4 0.3 0.4 0.4
[1] 3h82.a 0.5 0.5 0.3
0
0.5 0.4 0.6 0.5
[1] 4ghi.a 0.3 0.3 0.4 0.5
0
0.2 0.2 0.3
[1] 4gs9.a 0.2 0.3 0.3 0.4 0.2
0
0.3 0.3
[1] 5tbm.a 0.3 0.3 0.4 0.6 0.2 0.3
0
0.1
[1] 5ufp.a 0.4 0.3 0.4 0.5 0.3 0.3 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3f1n.a
3f1o.a
3h7w.a
3h82.a
4ghi.a
4gs9.a
5tbm.a
5ufp.a
[1] 3f1n.a
0
0.9 0.5 0.6 0.5 0.5 1.0 0.8
[1] 3f1o.a 0.9
0
0.9 0.9 0.9 1.0 1.1 0.9
[1] 3h7w.a 0.5 0.9
0
0.4 0.4 0.6 0.8 0.6
[1] 3h82.a 0.6 0.9 0.4
0
0.6 0.7 0.9 0.6
[1] 4ghi.a 0.5 0.9 0.4 0.6
0
0.5 0.8 0.5
[1] 4gs9.a 0.5 1.0 0.6 0.7 0.5
0
0.9 0.8
[1] 5tbm.a 1.0 1.1 0.8 0.9 0.8 0.9
0
0.6
[1] 5ufp.a 0.8 0.9 0.6 0.6 0.5 0.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...