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PTR1_LEIMA_1_288

Pteridine reductase 1 [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains homodimer
A1 (PTR1_LEIMA):17, 111, 113:115, 181:189, 191, 194, 225, 226, 229, 230, 232:234, 237, 241, 244, 28317, 111, 113:115, 181:189, 191, 194, 225, 226, 229, 230, 232:234, 237, 241, 244, 283
A3 (PTR1_LEIMA):287, 288287, 288
Cofactors (cF):nap/ndp

Full PDB list

1e7w, 1e92, 1w0c, 2bf7, 2bfa, 2bfm, 2bfo, 2bfp, 2qhx, 2xox, 3h4v, 5l42, 5l4n (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A3 cF
R
1
7
S
1
1
1
F
1
1
3
P
1
1
5
D
1
8
1
L
1
8
8
Y
1
9
1
Y
1
9
4
G
2
2
5
L
2
2
6
L
2
2
9
D
2
3
2
M
2
3
3
H
2
4
1
Y
2
8
3
R
2
8
7
[1]1e7w.a mtx33 . . . . . . . . . . . . . . . . ndp
[1]1e92.a hbi17 . . . . . . . . . . . . . . . . nap
[1]1w0c.a taq13 . . . . . . . . . . . . . . . . nap
[1]2bfa.a cb335 . . . . . . . . . . . . . . . . ndp
[1]2bfm.b top21 . . . . . . . . . . . . . . . . ndp
[1]2bfp.a h4b17 . . . . . . . . . . . . . . . . nap
[1]2qhx.b fe133 . . . . . . . . . . . . . . . . nap
[1]3h4v.a dvp32 . . . . . . . . . . . . . . . . nap
[1]5l42.a 6j620 . . . . . . . . . . . . . . . . ndp
[1]5l4n.a 6qt19 . . . . . . . . . . . - - . . . ndp
[1]5l4n.d none . . . . . . . . . . . . . . . . ndp
[2]2xox.b 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 A3 cF
R
1
7
S
1
1
1
F
1
1
3
Y
1
1
4
P
1
1
5
D
1
8
1
A
1
8
2
M
1
8
3
T
1
8
4
N
1
8
5
Q
1
8
6
P
1
8
7
L
1
8
8
L
1
8
9
Y
1
9
1
Y
1
9
4
G
2
2
5
L
2
2
6
L
2
2
9
V
2
3
0
D
2
3
2
M
2
3
3
P
2
3
4
V
2
3
7
H
2
4
1
K
2
4
4
Y
2
8
3
R
2
8
7
A
2
8
8
[1]1e7w.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]1e92.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . nap
[1]1w0c.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . nap
[1]2bfa.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]2bfm.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]2bfp.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . nap
[1]2qhx.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . nap
[1]3h4v.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . nap
[1]5l42.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]5l4n.a . . . . . . . . . . . . . . . . . . . . - - - - . . . . . ndp
[1]5l4n.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[2]2xox.b . - - - - . * * * S . . . . . . . . - - - - - - - - - - -

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
1e7w.a:mtx
1e92.a:hbi
1w0c.a:taq
2bfa.a:cb3
2bfm.b:top
2bfp.a:h4b
2qhx.b:fe1
3h4v.a:dvp
5l42.a:6j6
5l4n.a:6qt
5l4n.d is apo
2xox.b is apo
[1] 1e7w.a
0.1
0 0.1 0.9 0.3 0 0.2 0.1 0.3 0.2 - -
[1] 1e92.a 0
0
0 0.3 0 0 0 0 0.3 0.1 - -
[1] 1w0c.a 0.1 0
0
0.2 0 0 0 0 0.4 0 - -
[1] 2bfa.a 0 0 0
0.2
0.1 0 0 0 0.3 0.1 - -
[1] 2bfm.b 0.1 0 0 0.4
0
0 0.1 0 0.3 0 - -
[1] 2bfp.a 0 0 0 0.3 0
0
0 0 0.3 0.1 - -
[1] 2qhx.b 0 0 0 0.2 0 0
0
0 0.3 0.1 - -
[1] 3h4v.a 0 0 0 0.3 0 0 0
0
0.3 0.1 - -
[1] 5l42.a 0.3 0 0 0.7 0.1 0 0.1 0
0
0.1 - -
[1] 5l4n.a 0.3 0.1 0 0.3 0 0.1 0.3 0 0.3
0
- -
[1] 5l4n.d 0.1 0.1 0.1 0.3 0 0 0.1 0 0.3 0.1
-
-
[2] 2xox.b 7.2 8.1 6.0 8.2 6.7 8.7 7.8 8.1 6.1 7.4 -
-
[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
1e7w.a
1e92.a
1w0c.a
2bfa.a
2bfm.b
2bfp.a
2qhx.b
3h4v.a
5l42.a
5l4n.a
5l4n.d
2xox.b
[1] 1e7w.a
0
.03 .03 .02 .03 .03 .03 .03 .05 .04 .04 .40
[1] 1e92.a .03
0
.01 .01 .01 0 0 0 .03 .01 .01 .37
[1] 1w0c.a .03 .01
0
.01 .01 .01 0 .01 .03 .01 .01 .37
[1] 2bfa.a .02 .01 .01
0
.01 .01 0 .01 .03 .01 .01 .37
[1] 2bfm.b .03 .01 .01 .01
0
.01 .01 .01 .02 .02 .01 .38
[1] 2bfp.a .03 0 .01 .01 .01
0
0 0 .03 .01 .01 .37
[1] 2qhx.b .03 0 0 0 .01 0
0
0 .03 .01 .01 .37
[1] 3h4v.a .03 0 .01 .01 .01 0 0
0
.03 .01 .01 .37
[1] 5l42.a .05 .03 .03 .03 .02 .03 .03 .03
0
.03 .03 .38
[1] 5l4n.a .04 .01 .01 .01 .02 .01 .01 .01 .03
0
.01 .38
[1] 5l4n.d .04 .01 .01 .01 .01 .01 .01 .01 .03 .01
0
.38
[2] 2xox.b .40 .37 .37 .37 .38 .37 .37 .37 .38 .38 .38
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

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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
1e7w.a
1e92.a
1w0c.a
2bfa.a
2bfm.b
2bfp.a
2qhx.b
3h4v.a
5l42.a
5l4n.a
5l4n.d
2xox.b
[1] 1e7w.a
0
1.6 1.8 1.6 1.8 1.6 1.7 1.6 1.5 0.5 1.5 9.3
[1] 1e92.a 1.6
0
0.5 0.2 0.5 0.1 0.4 0.2 0.3 0.7 0.2 9.2
[1] 1w0c.a 1.8 0.5
0
0.3 0.7 0.5 0.4 0.3 0.5 0.5 0.5 9.3
[1] 2bfa.a 1.6 0.2 0.3
0
0.5 0.2 0.4 0.2 0.3 0.6 0.2 9.3
[1] 2bfm.b 1.8 0.5 0.7 0.5
0
0.5 0.5 0.5 0.6 0.7 0.5 9.4
[1] 2bfp.a 1.6 0.1 0.5 0.2 0.5
0
0.5 0.3 0.3 0.7 0.2 9.2
[1] 2qhx.b 1.7 0.4 0.4 0.4 0.5 0.5
0
0.3 0.5 0.4 0.4 9.3
[1] 3h4v.a 1.6 0.2 0.3 0.2 0.5 0.3 0.3
0
0.3 0.6 0.3 9.3
[1] 5l42.a 1.5 0.3 0.5 0.3 0.6 0.3 0.5 0.3
0
0.5 0.2 9.3
[1] 5l4n.a 0.5 0.7 0.5 0.6 0.7 0.7 0.4 0.6 0.5
0
0.6 9.3
[1] 5l4n.d 1.5 0.2 0.5 0.2 0.5 0.2 0.4 0.3 0.2 0.6
0
9.2
[2] 2xox.b 9.3 9.2 9.3 9.3 9.4 9.2 9.3 9.3 9.3 9.3 9.2
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
1e7w.a
1e92.a
1w0c.a
2bfa.a
2bfm.b
2bfp.a
2qhx.b
3h4v.a
5l42.a
5l4n.a
5l4n.d
2xox.b
[1] 1e7w.a
0
1.7 1.9 1.8 1.9 1.7 1.8 1.8 1.6 0.6 1.7 9.7
[1] 1e92.a 1.7
0
0.6 0.4 0.6 0.2 0.5 0.3 0.5 0.7 0.4 9.7
[1] 1w0c.a 1.9 0.6
0
0.6 0.8 0.6 0.6 0.5 0.8 0.7 0.6 9.7
[1] 2bfa.a 1.8 0.4 0.6
0
0.7 0.4 0.6 0.4 0.6 0.7 0.5 9.7
[1] 2bfm.b 1.9 0.6 0.8 0.7
0
0.5 0.6 0.6 0.8 0.8 0.6 9.8
[1] 2bfp.a 1.7 0.2 0.6 0.4 0.5
0
0.6 0.3 0.6 0.7 0.4 9.7
[1] 2qhx.b 1.8 0.5 0.6 0.6 0.6 0.6
0
0.5 0.7 0.6 0.5 9.7
[1] 3h4v.a 1.8 0.3 0.5 0.4 0.6 0.3 0.5
0
0.6 0.7 0.4 9.8
[1] 5l42.a 1.6 0.5 0.8 0.6 0.8 0.6 0.7 0.6
0
0.8 0.5 9.8
[1] 5l4n.a 0.6 0.7 0.7 0.7 0.8 0.7 0.6 0.7 0.8
0
0.7 9.8
[1] 5l4n.d 1.7 0.4 0.6 0.5 0.6 0.4 0.5 0.4 0.5 0.7
0
9.7
[2] 2xox.b 9.7 9.7 9.7 9.7 9.8 9.7 9.7 9.8 9.8 9.8 9.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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