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DDAH1_HUMAN_2_285

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 [DDAH family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DDAH1_HUMAN):R: Substrate binding (78, 79)
30:32, 73, 76, 98, 129, 145, 172, 173, 175, 176, 221, 268:271, 273, 274
30:32, 73, 76, 78, 79, 98, 129, 145, 172, 173, 175, 176, 221, 268:271, 273, 274

Full PDB list

2c6z, 2ci1, 2ci3, 2ci4, 2ci5, 2ci6, 2ci7, 2jai, 2jaj, 3i2e, 3i4a, 3p8e, 3p8p (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
3
0
D
7
3
F
7
6
E
7
8
D
7
9
R
9
8
G
1
2
9
R
1
4
5
L
1
7
2
H
1
7
3
K
1
7
5
S
1
7
6
N
2
2
1
V
2
6
8
D
2
6
9
G
2
7
0
L
2
7
1
T
2
7
3
C
2
7
4
[1]2c6z.a cir12 . . . . . . . . . . . . . . . . . . .
[1]2ci3.a none . . . . . . . . . . . . . . . . . . .
[1]2ci5.a hcs8 . . . . . . . . . . . . . . . . . . .
[1]2ci6.a zn1 . . . . . . . . . . . . . . . . . . .
[1]2ci7.a G,zn6 . . . . . . . . . . . . . . . . . . .
[1]2jai.a cir12 . . . . . . . . . . . . . . . . . . .
[1]2jaj.a d2016 . . . . . . . . . . . . . . . . . . .
[1]3i2e.a none . . . . . . . . . . . . . . . . . . .
[1]3i4a.a ln513 . . . . . . . . . . . . . . . . . . *
[1]3p8e.a ln715 . . . . . . . . . . . . . . . . . . *
[1]3p8p.a ln615 . . . . . . . . . . . . . . . . . . S
[2]2ci1.a none . . . . . . . . . . . . . . . . . . *

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
L
3
0
R
3
1
S
3
2
D
7
3
F
7
6
E
7
8
D
7
9
R
9
8
G
1
2
9
R
1
4
5
L
1
7
2
H
1
7
3
K
1
7
5
S
1
7
6
N
2
2
1
V
2
6
8
D
2
6
9
G
2
7
0
L
2
7
1
T
2
7
3
C
2
7
4
[1]2c6z.a . . R . . . . . . . . * . . . . . . . . .
[1]2ci3.a . . R . . . . . . . . * . . . . . . . . *
[1]2ci5.a . . R . . . . . . . . * . . . . . . . . *
[1]2ci6.a . . R . . . . . . . . * . . . . . . . . *
[1]2ci7.a . . R . . . . . . . . . . . . . . . . . *
[1]2jai.a . . . . . . . . . . . * . . . . . . . . *
[1]2jaj.a . . . . . . . . . . . . . . . . . . . . *
[1]3i2e.a . . . . . . . . . . . . . . . . . . . . *
[1]3i4a.a . . . . . . . . . . . . . . . . . . . . *
[1]3p8e.a . . . . . . . . . . . . . . . . . . . . *
[1]3p8p.a . . . . . . . . . . . . . . . . . . . . S
[2]2ci1.a . . R . . . . . . . . * . . . . . . . . kor

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
2c6z.a:cir
2ci3.a is apo
2ci5.a:hcs
2ci6.a:zn
2ci7.a:G,zn
2jai.a:cir
2jaj.a:d20
3i2e.a is apo
3i4a.a:ln5
3p8e.a:ln7
3p8p.a:ln6
2ci1.a is apo
[1] 2c6z.a
0
- 0 0 0.1 0.1 1.2 - 0.4 1.1 0.9 -
[1] 2ci3.a 0.9
-
0.3 0.3 0.4 0.9 1.6 - 1.2 2.1 0.9 -
[1] 2ci5.a 0.6 -
0
0.3 0.4 0.5 1.4 - 0.7 1.5 1.1 -
[1] 2ci6.a 1.1 - 0.3
0.3
0.5 0.8 1.3 - 0.8 1.9 1.0 -
[1] 2ci7.a 0.6 - 0 0.1
0.1
0.5 0.8 - 0.4 1.2 0.5 -
[1] 2jai.a 0.6 - 0 0.3 0.2
0.4
0.9 - 0.4 1.3 0.7 -
[1] 2jaj.a 0.7 - 0.2 0.3 0.4 0.3
0.1
- 0.5 0.8 0.1 -
[1] 3i2e.a 0.7 - 0 0.3 0.4 0.6 0.2
-
0.4 0.6 0.2 -
[1] 3i4a.a 0.8 - 0.1 0.3 0.3 0.7 1.0 -
0.8
1.8 0.9 -
[1] 3p8e.a 0.7 - 0.2 0.3 0.3 0.6 0.3 - 0.5
0.8
0.2 -
[1] 3p8p.a 0.6 - 0 0.1 0.1 0.3 0.5 - 0.5 0.8
0.3
-
[2] 2ci1.a 7.3 - 6.4 0.7 5.9 7.4 6.8 - 7.4 8.4 7.0
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
2c6z.a
2ci3.a
2ci5.a
2ci6.a
2ci7.a
2jai.a
2jaj.a
3i2e.a
3i4a.a
3p8e.a
3p8p.a
2ci1.a
[1] 2c6z.a
0
.08 .05 .07 .07 .06 .10 .10 .06 .09 .09 .37
[1] 2ci3.a .08
0
.06 .04 .06 .07 .08 .10 .04 .08 .10 .35
[1] 2ci5.a .05 .06
0
.06 .04 .03 .08 .07 .05 .06 .09 .34
[1] 2ci6.a .07 .04 .06
0
.06 .05 .09 .09 .05 .09 .11 .37
[1] 2ci7.a .07 .06 .04 .06
0
.03 .04 .05 .02 .03 .05 .37
[1] 2jai.a .06 .07 .03 .05 .03
0
.06 .05 .03 .05 .07 .37
[1] 2jaj.a .10 .08 .08 .09 .04 .06
0
.03 .06 .02 .04 .40
[1] 3i2e.a .10 .10 .07 .09 .05 .05 .03
0
.07 .03 .03 .41
[1] 3i4a.a .06 .04 .05 .05 .02 .03 .06 .07
0
.05 .08 .36
[1] 3p8e.a .09 .08 .06 .09 .03 .05 .02 .03 .05
0
.02 .39
[1] 3p8p.a .09 .10 .09 .11 .05 .07 .04 .03 .08 .02
0
.41
[2] 2ci1.a .37 .35 .34 .37 .37 .37 .40 .41 .36 .39 .41
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
2c6z.a
2ci3.a
2ci5.a
2ci6.a
2ci7.a
2jai.a
2jaj.a
3i2e.a
3i4a.a
3p8e.a
3p8p.a
2ci1.a
[1] 2c6z.a
0
0.3 0.2 2.7 0.3 0.3 0.6 0.6 0.4 0.6 0.6 0.2
[1] 2ci3.a 0.3
0
0.3 2.6 0.4 0.4 0.5 0.6 0.5 0.6 0.5 0.3
[1] 2ci5.a 0.2 0.3
0
2.8 0.3 0.3 0.6 0.5 0.4 0.7 0.6 0.2
[1] 2ci6.a 2.7 2.6 2.8
0
2.7 2.8 2.7 2.9 2.8 2.7 2.8 2.7
[1] 2ci7.a 0.3 0.4 0.3 2.7
0
0.3 0.5 0.5 0.3 0.6 0.5 0.3
[1] 2jai.a 0.3 0.4 0.3 2.8 0.3
0
0.6 0.5 0.3 0.7 0.5 0.3
[1] 2jaj.a 0.6 0.5 0.6 2.7 0.5 0.6
0
0.6 0.5 0.4 0.4 0.6
[1] 3i2e.a 0.6 0.6 0.5 2.9 0.5 0.5 0.6
0
0.3 0.7 0.4 0.6
[1] 3i4a.a 0.4 0.5 0.4 2.8 0.3 0.3 0.5 0.3
0
0.7 0.4 0.4
[1] 3p8e.a 0.6 0.6 0.7 2.7 0.6 0.7 0.4 0.7 0.7
0
0.6 0.6
[1] 3p8p.a 0.6 0.5 0.6 2.8 0.5 0.5 0.4 0.4 0.4 0.6
0
0.5
[2] 2ci1.a 0.2 0.3 0.2 2.7 0.3 0.3 0.6 0.6 0.4 0.6 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2c6z.a
2ci3.a
2ci5.a
2ci6.a
2ci7.a
2jai.a
2jaj.a
3i2e.a
3i4a.a
3p8e.a
3p8p.a
2ci1.a
[1] 2c6z.a
0
0.7 0.5 4.1 0.6 0.5 1.4 1.3 1.1 1.2 1.3 0.9
[1] 2ci3.a 0.7
0
0.5 4.1 0.6 0.6 1.4 1.3 1.1 1.2 1.3 0.9
[1] 2ci5.a 0.5 0.5
0
4.2 0.5 0.5 1.5 1.3 1.1 1.2 1.3 0.9
[1] 2ci6.a 4.1 4.1 4.2
0
4.2 3.8 4.0 4.0 3.9 3.9 4.0 4.1
[1] 2ci7.a 0.6 0.6 0.5 4.2
0
0.5 1.4 1.2 1.1 1.1 1.2 0.8
[1] 2jai.a 0.5 0.6 0.5 3.8 0.5
0
1.4 1.2 1.1 1.2 1.3 0.5
[1] 2jaj.a 1.4 1.4 1.5 4.0 1.4 1.4
0
0.9 0.9 0.8 0.8 1.4
[1] 3i2e.a 1.3 1.3 1.3 4.0 1.2 1.2 0.9
0
0.5 0.8 0.5 1.3
[1] 3i4a.a 1.1 1.1 1.1 3.9 1.1 1.1 0.9 0.5
0
0.7 0.5 1.1
[1] 3p8e.a 1.2 1.2 1.2 3.9 1.1 1.2 0.8 0.8 0.7
0
0.7 1.2
[1] 3p8p.a 1.3 1.3 1.3 4.0 1.2 1.3 0.8 0.5 0.5 0.7
0
1.3
[2] 2ci1.a 0.9 0.9 0.9 4.1 0.8 0.5 1.4 1.3 1.1 1.2 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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