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DHB1_HUMAN_2_290

Estradiol 17-beta-dehydrogenase 1 [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (DHB1_HUMAN):9:17, 36:39, 42, 65:68, 91:95, 114, 141:145, 148, 150, 153, 156, 160, 186:189, 191:197, 219, 222, 223, 226, 227, 259, 260, 263, 280, 283, 2849:17, 36:39, 42, 65:68, 91:95, 114, 141:145, 148, 150, 153, 156, 160, 186:189, 191:197, 219, 222, 223, 226, 227, 259, 260, 263, 280, 283, 284

Full PDB list

1a27, 1bhs, 1dht, 1equ, 1fds, 1fdt, 1fdu, 1fdv, 1fdw, 1i5r, 1iol, 1jtv, 1qyv, 1qyw, 1qyx, 3dey, 3dhe, 3hb4, 3hb5, 3klm, 3klp, 3km0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
1
0
C
1
1
S
1
2
S
1
3
G
1
4
I
1
5
G
1
6
L
3
7
R
3
8
L
6
5
D
6
6
V
6
7
R
6
8
N
9
1
A
9
2
G
9
3
L
9
4
G
9
5
V
1
1
4
T
1
4
1
G
1
4
2
S
1
4
3
V
1
4
4
G
1
4
5
M
1
4
8
L
1
5
0
N
1
5
3
Y
1
5
6
K
1
6
0
C
1
8
6
G
1
8
7
P
1
8
8
V
1
8
9
T
1
9
1
A
1
9
2
F
1
9
3
M
1
9
4
E
1
9
5
K
1
9
6
Y
2
1
9
H
2
2
2
S
2
2
3
V
2
2
6
F
2
2
7
R
2
5
9
F
2
6
0
M
2
8
0
E
2
8
3
V
2
8
4
[1]1a27.a est,nap68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1bhs.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1dht.a dht21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1equ.a eqi,nap68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1fds.a est20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . . . . . .
[1]1fdu.c est,nap68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . L . . . . . . . .
[1]1fdv.a nad44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . L . . . . . . . .
[1]1fdw.a est20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - . Q . . . . . . . .
[1]1i5r.a hyc49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jtv.a tes21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . . . . . .
[1]1qyw.a 5sd,nap48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . . . . . .
[1]1qyx.a asd,nap48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . . . . . .
[1]3dhe.a and21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3hb4.x e2b30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3hb5.x nap48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3klp.x b8121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - . . . . . . . . . .
[1]3km0.b aom,nap69 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - . . . . . . . . . .

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
9
G
1
0
C
1
1
S
1
2
S
1
3
G
1
4
I
1
5
G
1
6
L
1
7
T
3
6
L
3
7
R
3
8
D
3
9
T
4
2
L
6
5
D
6
6
V
6
7
R
6
8
N
9
1
A
9
2
G
9
3
L
9
4
G
9
5
V
1
1
4
T
1
4
1
G
1
4
2
S
1
4
3
V
1
4
4
G
1
4
5
M
1
4
8
L
1
5
0
N
1
5
3
Y
1
5
6
K
1
6
0
C
1
8
6
G
1
8
7
P
1
8
8
V
1
8
9
T
1
9
1
A
1
9
2
F
1
9
3
M
1
9
4
E
1
9
5
K
1
9
6
V
1
9
7
Y
2
1
9
H
2
2
2
S
2
2
3
V
2
2
6
F
2
2
7
R
2
5
9
F
2
6
0
L
2
6
3
M
2
8
0
E
2
8
3
V
2
8
4
[1]1a27.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . - . . . . . . . . . . .
[1]1bhs.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]1dht.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1equ.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . .
[1]1fds.a . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . . . . . * . . . . . .
[1]1fdu.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . L . . * . . . . . .
[1]1fdv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . L . . * . * . . . .
[1]1fdw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . Q . . . . . . . . .
[1]1i5r.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . * . . * . . . . . .
[1]1jtv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - . . . . . . . . . . .
[1]1qyw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - . . . . . . . . . . .
[1]1qyx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - . . . . . . . . . . .
[1]3dhe.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]3hb4.x . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . * . . . . . .
[1]3hb5.x . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . * . . . . . .
[1]3klp.x . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - . . . . . . . . . . .
[1]3km0.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - . . . . * . . . . . .

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
1a27.a:est,nap
1bhs.a is apo
1dht.a:dht
1equ.a:eqi,nap
1fds.a:est
1fdu.c:est,nap
1fdv.a:nad
1fdw.a:est
1i5r.a:hyc
1jtv.a:tes
1qyw.a:5sd,nap
1qyx.a:asd,nap
3dhe.a:and
3hb4.x:e2b
3hb5.x:nap
3klp.x:b81
3km0.b:aom,nap
[1] 1a27.a
0.1
- 0.5 0.5 0.1 0.5 0.3 0.5 4.6 0.6 0.8 0.6 0.6 3.8 1.2 0.5 1.2
[1] 1bhs.a 1.3
-
0.4 1.2 0.2 1.5 0.7 0.1 0.5 1.1 0.8 0.8 0.6 0.5 1.1 0.3 2.0
[1] 1dht.a 0.7 -
0.1
0.6 0.1 1.2 0.6 0.5 0.5 1.0 1.2 1.1 0.9 0.6 0.9 0.6 1.9
[1] 1equ.a 0.9 - 0.5
1.3
0.1 0.6 0.3 0.5 4.6 0.4 0.5 0.3 0.7 4.2 1.4 0.2 2.0
[1] 1fds.a 0.6 - 0.3 0.8
0
1.2 0.2 0.2 0.3 1.6 1.4 1.4 1.1 0.2 0.7 0.7 1.1
[1] 1fdu.c 0.2 - 0.4 0.7 0.1
0.4
0.1 0.2 4.0 1.8 1.1 1.8 0.9 4.2 1.3 0.5 1.7
[1] 1fdv.a 1.2 - 0.6 1.1 0.7 1.2
0.2
0.5 4.5 1.6 1.0 1.4 0.5 4.1 0.4 0.5 1.4
[1] 1fdw.a 0.8 - 0.2 1.2 0.1 0.8 0.3
0
0.4 0.6 0.1 0.3 0.6 0.4 0.4 0.2 1.3
[1] 1i5r.a 4.1 - 1.0 4.3 0.1 4.1 2.8 0.8
0.2
2.4 4.4 4.6 2.4 0.4 2.8 1.5 3.5
[1] 1jtv.a 0.5 - 0.4 0.7 0.1 0.8 0.2 0.6 0.5
0
0.3 0.1 0.6 0.7 0.5 0.5 1.3
[1] 1qyw.a 0.7 - 0.2 0.6 0.1 1.0 0.3 0.1 0.6 0
0.1
0.1 0.4 0.6 0.6 0.2 1.4
[1] 1qyx.a 0.4 - 0.2 0.9 0.1 0.9 0.2 0.6 0.6 0 0.1
0
0.4 0.6 0.6 0.3 1.3
[1] 3dhe.a 0.6 - 0.2 0.7 0 1.0 0.1 0.5 0.3 1.0 0.7 1.0
0.6
0.4 0.5 0.2 1.3
[1] 3hb4.x 3.1 - 0.7 2.0 0 3.4 3.1 0.1 0.1 1.8 1.2 1.9 1.6
0
3.6 1.1 4.0
[1] 3hb5.x 0.8 - 0.6 1.5 0 1.4 0.3 0.1 2.9 1.6 2.6 2.4 1.2 2.9
0.4
0.6 1.2
[1] 3klp.x 2.0 - 0.3 2.2 0.1 2.2 1.6 0.6 1.7 0 1.4 1.4 0.2 0.3 2.1
0.1
2.2
[1] 3km0.b 0.4 - 0.2 0.5 0.1 0.7 0.3 0.4 0.5 1.2 0.8 1.1 0.7 0.1 0.5 0.7
0.9
[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
1a27.a
1bhs.a
1dht.a
1equ.a
1fds.a
1fdu.c
1fdv.a
1fdw.a
1i5r.a
1jtv.a
1qyw.a
1qyx.a
3dhe.a
3hb4.x
3hb5.x
3klp.x
3km0.b
[1] 1a27.a
0
.15 .17 .06 .16 .09 .11 .15 .14 .14 .14 .14 .16 .12 .12 .17 .16
[1] 1bhs.a .15
0
.06 .15 .09 .18 .15 .06 .17 .05 .05 .04 .04 .13 .15 .10 .08
[1] 1dht.a .17 .06
0
.15 .06 .17 .15 .06 .15 .05 .04 .05 .05 .13 .15 .09 .06
[1] 1equ.a .06 .15 .15
0
.17 .11 .11 .14 .14 .13 .14 .13 .16 .12 .12 .17 .16
[1] 1fds.a .16 .09 .06 .17
0
.14 .13 .06 .13 .08 .06 .07 .09 .10 .11 .08 .05
[1] 1fdu.c .09 .18 .17 .11 .14
0
.08 .14 .13 .18 .16 .16 .18 .10 .10 .18 .15
[1] 1fdv.a .11 .15 .15 .11 .13 .08
0
.13 .14 .15 .14 .14 .17 .10 .09 .17 .12
[1] 1fdw.a .15 .06 .06 .14 .06 .14 .13
0
.16 .05 .04 .05 .07 .12 .14 .09 .06
[1] 1i5r.a .14 .17 .15 .14 .13 .13 .14 .16
0
.17 .16 .18 .17 .08 .10 .20 .15
[1] 1jtv.a .14 .05 .05 .13 .08 .18 .15 .05 .17
0
.03 .02 .05 .13 .15 .07 .07
[1] 1qyw.a .14 .05 .04 .14 .06 .16 .14 .04 .16 .03
0
.02 .05 .12 .14 .06 .06
[1] 1qyx.a .14 .04 .05 .13 .07 .16 .14 .05 .18 .02 .02
0
.04 .13 .14 .06 .07
[1] 3dhe.a .16 .04 .05 .16 .09 .18 .17 .07 .17 .05 .05 .04
0
.14 .16 .08 .09
[1] 3hb4.x .12 .13 .13 .12 .10 .10 .10 .12 .08 .13 .12 .13 .14
0
.06 .17 .12
[1] 3hb5.x .12 .15 .15 .12 .11 .10 .09 .14 .10 .15 .14 .14 .16 .06
0
.13 .13
[1] 3klp.x .17 .10 .09 .17 .08 .18 .17 .09 .20 .07 .06 .06 .08 .17 .13
0
.10
[1] 3km0.b .16 .08 .06 .16 .05 .15 .12 .06 .15 .07 .06 .07 .09 .12 .13 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1a27.a
1bhs.a
1dht.a
1equ.a
1fds.a
1fdu.c
1fdv.a
1fdw.a
1i5r.a
1jtv.a
1qyw.a
1qyx.a
3dhe.a
3hb4.x
3hb5.x
3klp.x
3km0.b
[1] 1a27.a
0
1.6 1.9 0.7 0.7 0.4 0.6 0.9 1.4 0.7 0.6 0.7 1.8 0.8 0.9 0.6 0.5
[1] 1bhs.a 1.6
0
1.1 1.7 1.0 1.9 2.0 0.4 2.6 0.5 0.5 0.5 1.0 2.0 1.8 0.4 0.6
[1] 1dht.a 1.9 1.1
0
1.9 0.8 2.0 2.1 0.7 2.3 0.6 0.6 0.6 0.4 2.0 1.7 0.3 0.7
[1] 1equ.a 0.7 1.7 1.9
0
0.7 0.7 0.8 0.9 1.6 0.6 0.6 0.6 1.8 1.1 1.1 0.5 0.5
[1] 1fds.a 0.7 1.0 0.8 0.7
0
0.7 0.7 0.4 0.9 0.4 0.3 0.3 0.7 0.5 0.5 0.3 0.6
[1] 1fdu.c 0.4 1.9 2.0 0.7 0.7
0
0.5 0.9 1.6 0.6 0.6 0.6 2.0 0.9 0.9 0.5 0.5
[1] 1fdv.a 0.6 2.0 2.1 0.8 0.7 0.5
0
0.8 1.5 0.7 0.7 0.7 2.0 0.8 0.9 0.6 0.5
[1] 1fdw.a 0.9 0.4 0.7 0.9 0.4 0.9 0.8
0
0.8 0.6 0.6 0.6 0.6 0.6 0.6 0.5 0.7
[1] 1i5r.a 1.4 2.6 2.3 1.6 0.9 1.6 1.5 0.8
0
0.6 0.5 0.6 2.4 1.3 1.5 0.5 0.7
[1] 1jtv.a 0.7 0.5 0.6 0.6 0.4 0.6 0.7 0.6 0.6
0
0.1 0.1 0.6 0.4 0.4 0.3 0.6
[1] 1qyw.a 0.6 0.5 0.6 0.6 0.3 0.6 0.7 0.6 0.5 0.1
0
0.1 0.6 0.3 0.3 0.2 0.6
[1] 1qyx.a 0.7 0.5 0.6 0.6 0.3 0.6 0.7 0.6 0.6 0.1 0.1
0
0.6 0.3 0.3 0.3 0.5
[1] 3dhe.a 1.8 1.0 0.4 1.8 0.7 2.0 2.0 0.6 2.4 0.6 0.6 0.6
0
1.9 1.7 0.3 0.6
[1] 3hb4.x 0.8 2.0 2.0 1.1 0.5 0.9 0.8 0.6 1.3 0.4 0.3 0.3 1.9
0
0.6 0.4 0.6
[1] 3hb5.x 0.9 1.8 1.7 1.1 0.5 0.9 0.9 0.6 1.5 0.4 0.3 0.3 1.7 0.6
0
0.3 0.5
[1] 3klp.x 0.6 0.4 0.3 0.5 0.3 0.5 0.6 0.5 0.5 0.3 0.2 0.3 0.3 0.4 0.3
0
0.6
[1] 3km0.b 0.5 0.6 0.7 0.5 0.6 0.5 0.5 0.7 0.7 0.6 0.6 0.5 0.6 0.6 0.5 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1a27.a
1bhs.a
1dht.a
1equ.a
1fds.a
1fdu.c
1fdv.a
1fdw.a
1i5r.a
1jtv.a
1qyw.a
1qyx.a
3dhe.a
3hb4.x
3hb5.x
3klp.x
3km0.b
[1] 1a27.a
0
2.1 2.8 1.5 1.1 0.9 1.1 1.2 2.4 1.0 1.2 1.0 2.7 1.5 1.3 1.1 0.8
[1] 1bhs.a 2.1
0
1.8 2.4 1.5 2.4 2.5 1.1 3.2 1.0 1.1 0.9 1.7 2.6 2.3 1.0 1.1
[1] 1dht.a 2.8 1.8
0
2.9 1.3 2.9 3.0 1.1 3.0 1.0 0.9 0.9 0.8 2.8 2.5 1.0 1.1
[1] 1equ.a 1.5 2.4 2.9
0
1.5 1.6 1.6 1.6 2.6 1.4 1.4 1.4 2.8 1.8 1.7 1.5 1.4
[1] 1fds.a 1.1 1.5 1.3 1.5
0
1.2 1.1 0.7 1.1 1.0 1.1 1.0 1.2 1.0 0.9 1.0 0.9
[1] 1fdu.c 0.9 2.4 2.9 1.6 1.2
0
1.0 1.3 2.5 1.1 1.2 1.1 2.9 1.5 1.3 1.1 0.8
[1] 1fdv.a 1.1 2.5 3.0 1.6 1.1 1.0
0
1.3 2.6 1.2 1.3 1.2 2.9 1.6 1.4 1.2 1.0
[1] 1fdw.a 1.2 1.1 1.1 1.6 0.7 1.3 1.3
0
1.1 1.0 1.1 1.0 1.0 1.0 1.1 1.0 1.1
[1] 1i5r.a 2.4 3.2 3.0 2.6 1.1 2.5 2.6 1.1
0
0.9 1.0 0.8 3.0 2.2 2.3 1.0 0.9
[1] 1jtv.a 1.0 1.0 1.0 1.4 1.0 1.1 1.2 1.0 0.9
0
0.7 0.3 0.9 0.9 1.0 0.8 0.9
[1] 1qyw.a 1.2 1.1 0.9 1.4 1.1 1.2 1.3 1.1 1.0 0.7
0
0.6 0.9 1.0 1.1 0.9 1.1
[1] 1qyx.a 1.0 0.9 0.9 1.4 1.0 1.1 1.2 1.0 0.8 0.3 0.6
0
0.9 0.9 1.0 0.8 0.9
[1] 3dhe.a 2.7 1.7 0.8 2.8 1.2 2.9 2.9 1.0 3.0 0.9 0.9 0.9
0
2.8 2.5 0.9 1.0
[1] 3hb4.x 1.5 2.6 2.8 1.8 1.0 1.5 1.6 1.0 2.2 0.9 1.0 0.9 2.8
0
1.1 0.9 0.9
[1] 3hb5.x 1.3 2.3 2.5 1.7 0.9 1.3 1.4 1.1 2.3 1.0 1.1 1.0 2.5 1.1
0
0.9 0.8
[1] 3klp.x 1.1 1.0 1.0 1.5 1.0 1.1 1.2 1.0 1.0 0.8 0.9 0.8 0.9 0.9 0.9
0
0.9
[1] 3km0.b 0.8 1.1 1.1 1.4 0.9 0.8 1.0 1.1 0.9 0.9 1.1 0.9 1.0 0.9 0.8 0.9
0
[Binding site full-atom RMSD matrix]







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