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AK1D1_HUMAN_2_326

3-oxo-5-beta-steroid 4-dehydrogenase [Aldo/keto reductase family]

Composition of the binding site

Protein chains monomer
A1 (AK1D1_HUMAN):26, 57, 58, 89, 120, 132, 134, 140, 224:227, 229:231, 309, 311, 313, 31426, 57, 58, 89, 120, 132, 134, 140, 224:227, 229:231, 309, 311, 313, 314
Cofactors (cF):nap

Full PDB list

3bur, 3buv, 3bv7, 3caq, 3cas, 3cav, 3cmf, 3cot, 3dop, 3g1r, 3uzw, 3uzx, 3uzy, 3uzz (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
Y
2
6
I
5
7
Y
5
8
W
8
9
E
1
2
0
Y
1
3
2
R
1
3
4
W
1
4
0
T
2
2
4
S
2
2
5
R
2
2
6
N
2
2
7
I
2
2
9
W
2
3
0
V
2
3
1
V
3
0
9
L
3
1
1
M
3
1
3
W
3
1
4
[1]3bur.a tes21 . . . . . . . . . . . . . . . . . . . nap
[1]3buv.a none . . . . . . . . . . . . . . . . . . . nap
[1]3cas.a asd21 . . . . . . . . . . . . . . . . . . . nap
[1]3cav.b ci223 . . . . . . . . . . . . . . . . . . . nap
[1]3cmf.a pdn26 . . . . . . . . . . . . . . . . . . . nap
[1]3cot.a str23 . . . . . . . . . . . . . . . . . . . nap
[1]3dop.b bdt21 . . . . . . . . . . . . . . . . . . . nap
[1]3g1r.b fit27 . . . . . . . . . . . . . . . . . . . nap
[1]3uzw.a none . . . . H . . . . . . . . . . . . . . nap
[1]3uzx.a aom21 . . . . H . . . . . . . . . . . . . . nap
[1]3uzx.b aox21 . . . . H . . . . . . . . . . . . . . nap
[1]3uzy.a bdt21 . . . . H . . . . . . . . . . . . . . nap
[1]3uzz.a tes21 . . . . H . . . . . . . . . . . . . . nap
[1]3uzz.b asd21 . . . . H . . . . . . . . . . . . . . nap

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 cF
Y
2
6
I
5
7
Y
5
8
W
8
9
E
1
2
0
Y
1
3
2
R
1
3
4
W
1
4
0
T
2
2
4
S
2
2
5
R
2
2
6
N
2
2
7
I
2
2
9
W
2
3
0
V
2
3
1
V
3
0
9
L
3
1
1
M
3
1
3
W
3
1
4
[1]3bur.a . . . . . . . . . . . . . * . . . . . nap
[1]3buv.a . . . . . * . . . . . . . * . . . . . nap
[1]3cas.a . . . . . . . . . . . . . * . . . . . nap
[1]3cav.b . . . . . . . . . . . . . * . . . . . nap
[1]3cmf.a . . . . . . . . . . . . . * . . . . . nap
[1]3cot.a . . . . . . . . . . . . . * . . . . . nap
[1]3dop.b . . . . . . . . . . . . . * . . . . . nap
[1]3g1r.b . . . . . . . . . . . . . * . . . . . nap
[1]3uzw.a . . . . H . . . . . . . . * . . . . . nap
[1]3uzx.a . . . . H . . . . . . . . * . . . . . nap
[1]3uzx.b . . . . H . . . . . . . . * . . . . . nap
[1]3uzy.a . . . . H . . . . . . . . * . . . . . nap
[1]3uzz.a . . . . H . . . . . . . . * . . . . . nap
[1]3uzz.b . . . . H . . . . . . . . * . . . . . nap

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
3bur.a:tes
3buv.a is apo
3cas.a:asd
3cav.b:ci2
3cmf.a:pdn
3cot.a:str
3dop.b:bdt
3g1r.b:fit
3uzw.a is apo
3uzx.a:aom
3uzx.b:aox
3uzy.a:bdt
3uzz.a:tes
3uzz.b:asd
[1] 3bur.a
0
- 0.2 2.5 3.7 3.1 4.1 4.1 - 2.7 2.1 2.6 2.9 2.7
[1] 3buv.a 0.6
-
0.9 3.9 4.7 4.2 5.0 5.0 - 3.9 3.4 3.4 3.8 3.7
[1] 3cas.a 0 -
0
3.1 4.2 3.5 5.0 4.6 - 3.3 2.6 3.1 3.3 3.5
[1] 3cav.b 3.0 - 2.8
0
0 0 0 0.1 - 0 0 0 0 0
[1] 3cmf.a 3.9 - 3.2 0.1
0
0 0.1 0.2 - 0 0 0.1 0 0
[1] 3cot.a 3.6 - 2.8 0.3 0
0
0.2 0.3 - 0 0 0.1 0 0.1
[1] 3dop.b 2.5 - 2.1 0.1 0 0
0
0 - 0 0 0 0 0
[1] 3g1r.b 2.5 - 2.0 0.4 0.2 0 0.2
0
- 0.1 0.1 0 0 0
[1] 3uzw.a 0.2 - 0.3 4.0 4.5 3.9 4.4 5.0
-
3.1 2.8 3.4 2.8 2.7
[1] 3uzx.a 3.2 - 3.0 0.8 0.8 0.7 0.4 0.9 -
0
0 0.1 0 0.1
[1] 3uzx.b 3.5 - 3.2 0.6 0.8 0.7 0.5 1.0 - 0
0
0.1 0.1 0.1
[1] 3uzy.a 3.6 - 2.8 0.8 0.8 0.7 0.3 1.0 - 0 0
0
0 0
[1] 3uzz.a 3.6 - 3.4 0.6 1.0 0.9 0.4 1.2 - 0.1 0.1 0.1
0.1
0.1
[1] 3uzz.b 3.5 - 3.4 0.6 0.7 0.8 0.1 0.7 - 0.1 0.1 0.1 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
3bur.a
3buv.a
3cas.a
3cav.b
3cmf.a
3cot.a
3dop.b
3g1r.b
3uzw.a
3uzx.a
3uzx.b
3uzy.a
3uzz.a
3uzz.b
[1] 3bur.a
0
.11 .05 .11 .09 .10 .16 .16 .08 .12 .15 .12 .10 .09
[1] 3buv.a .11
0
.08 .20 .18 .19 .25 .25 .12 .21 .24 .21 .20 .19
[1] 3cas.a .05 .08
0
.15 .13 .14 .19 .18 .08 .14 .17 .16 .14 .13
[1] 3cav.b .11 .20 .15
0
.04 .04 .07 .10 .17 .08 .08 .09 .09 .09
[1] 3cmf.a .09 .18 .13 .04
0
.02 .09 .11 .14 .10 .07 .07 .07 .07
[1] 3cot.a .10 .19 .14 .04 .02
0
.08 .11 .16 .09 .06 .07 .09 .08
[1] 3dop.b .16 .25 .19 .07 .09 .08
0
.03 .22 .12 .12 .14 .16 .14
[1] 3g1r.b .16 .25 .18 .10 .11 .11 .03
0
.20 .11 .12 .12 .15 .13
[1] 3uzw.a .08 .12 .08 .17 .14 .16 .22 .20
0
.11 .13 .10 .08 .08
[1] 3uzx.a .12 .21 .14 .08 .10 .09 .12 .11 .11
0
.04 .05 .05 .04
[1] 3uzx.b .15 .24 .17 .08 .07 .06 .12 .12 .13 .04
0
.04 .06 .07
[1] 3uzy.a .12 .21 .16 .09 .07 .07 .14 .12 .10 .05 .04
0
.03 .04
[1] 3uzz.a .10 .20 .14 .09 .07 .09 .16 .15 .08 .05 .06 .03
0
.02
[1] 3uzz.b .09 .19 .13 .09 .07 .08 .14 .13 .08 .04 .07 .04 .02
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

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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
3bur.a
3buv.a
3cas.a
3cav.b
3cmf.a
3cot.a
3dop.b
3g1r.b
3uzw.a
3uzx.a
3uzx.b
3uzy.a
3uzz.a
3uzz.b
[1] 3bur.a
0
0.4 0.3 0.9 0.7 0.7 1.0 1.1 0.4 0.7 0.7 0.7 0.7 0.6
[1] 3buv.a 0.4
0
0.3 0.9 0.6 0.6 1.0 1.0 0.2 0.6 0.6 0.6 0.7 0.6
[1] 3cas.a 0.3 0.3
0
0.7 0.5 0.5 0.9 0.9 0.3 0.6 0.5 0.5 0.6 0.4
[1] 3cav.b 0.9 0.9 0.7
0
0.4 0.4 0.4 0.5 0.9 0.6 0.5 0.5 0.8 0.5
[1] 3cmf.a 0.7 0.6 0.5 0.4
0
0.2 0.5 0.6 0.6 0.3 0.3 0.3 0.5 0.3
[1] 3cot.a 0.7 0.6 0.5 0.4 0.2
0
0.6 0.6 0.6 0.4 0.3 0.3 0.6 0.3
[1] 3dop.b 1.0 1.0 0.9 0.4 0.5 0.6
0
0.2 0.9 0.7 0.6 0.6 0.8 0.6
[1] 3g1r.b 1.1 1.0 0.9 0.5 0.6 0.6 0.2
0
1.0 0.7 0.6 0.6 0.8 0.6
[1] 3uzw.a 0.4 0.2 0.3 0.9 0.6 0.6 0.9 1.0
0
0.6 0.6 0.6 0.6 0.5
[1] 3uzx.a 0.7 0.6 0.6 0.6 0.3 0.4 0.7 0.7 0.6
0
0.4 0.3 0.3 0.4
[1] 3uzx.b 0.7 0.6 0.5 0.5 0.3 0.3 0.6 0.6 0.6 0.4
0
0.3 0.5 0.2
[1] 3uzy.a 0.7 0.6 0.5 0.5 0.3 0.3 0.6 0.6 0.6 0.3 0.3
0
0.4 0.3
[1] 3uzz.a 0.7 0.7 0.6 0.8 0.5 0.6 0.8 0.8 0.6 0.3 0.5 0.4
0
0.5
[1] 3uzz.b 0.6 0.6 0.4 0.5 0.3 0.3 0.6 0.6 0.5 0.4 0.2 0.3 0.5
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

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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
3bur.a
3buv.a
3cas.a
3cav.b
3cmf.a
3cot.a
3dop.b
3g1r.b
3uzw.a
3uzx.a
3uzx.b
3uzy.a
3uzz.a
3uzz.b
[1] 3bur.a
0
0.5 0.6 1.4 1.2 1.2 1.4 1.4 0.6 1.2 1.2 1.2 1.2 1.2
[1] 3buv.a 0.5
0
0.6 1.4 1.2 1.2 1.4 1.4 0.3 1.2 1.2 1.2 1.2 1.2
[1] 3cas.a 0.6 0.6
0
1.3 1.2 1.2 1.3 1.3 0.6 1.2 1.1 1.2 1.2 1.1
[1] 3cav.b 1.4 1.4 1.3
0
0.6 0.7 0.6 0.7 1.4 0.8 0.7 0.7 0.9 0.7
[1] 3cmf.a 1.2 1.2 1.2 0.6
0
0.3 0.6 0.6 1.1 0.5 0.4 0.4 0.6 0.5
[1] 3cot.a 1.2 1.2 1.2 0.7 0.3
0
0.7 0.7 1.1 0.5 0.5 0.5 0.6 0.6
[1] 3dop.b 1.4 1.4 1.3 0.6 0.6 0.7
0
0.4 1.3 0.7 0.6 0.7 0.9 0.6
[1] 3g1r.b 1.4 1.4 1.3 0.7 0.6 0.7 0.4
0
1.3 0.7 0.6 0.6 0.9 0.6
[1] 3uzw.a 0.6 0.3 0.6 1.4 1.1 1.1 1.3 1.3
0
1.0 1.1 1.1 1.1 1.1
[1] 3uzx.a 1.2 1.2 1.2 0.8 0.5 0.5 0.7 0.7 1.0
0
0.5 0.5 0.5 0.6
[1] 3uzx.b 1.2 1.2 1.1 0.7 0.4 0.5 0.6 0.6 1.1 0.5
0
0.4 0.7 0.3
[1] 3uzy.a 1.2 1.2 1.2 0.7 0.4 0.5 0.7 0.6 1.1 0.5 0.4
0
0.5 0.4
[1] 3uzz.a 1.2 1.2 1.2 0.9 0.6 0.6 0.9 0.9 1.1 0.5 0.7 0.5
0
0.6
[1] 3uzz.b 1.2 1.2 1.1 0.7 0.5 0.6 0.6 0.6 1.1 0.6 0.3 0.4 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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