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DYR_CANAX_1_192

Dihydrofolate reductase [Dihydrofolate reductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYR_CANAX):D: DHFR (9:11, 24, 25, 32, 33, 36, 37, 54, 58, 61:63, 66, 69, 70, 112, 118, 133)
R: Substrate binding (32, 33, 36, 37)
9:11, 24, 25, 32, 33, 36, 37, 54, 58, 61:63, 66, 69, 70, 112, 118, 133
Cofactors (cF):ndp

Full PDB list

1ai9, 1aoe, 1ia1, 1ia2, 1ia3, 1ia4, 1m78, 1m79, 1m7a, 3qlr, 3qls, 3qlw, 4h95, 4h96, 4h97, 4hoe, 4hof (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
I
9
V
1
0
A
1
1
M
2
5
E
3
2
I
3
3
F
3
6
K
3
7
T
5
8
S
6
1
I
6
2
P
6
3
F
6
6
L
6
9
I
1
1
2
Y
1
1
8
[1]1aoe.a gw320 . . . . . . . . . . . . . . . . ndp
[1]1ia1.b tq319 . . . . . . . . . . . . . . . . ndp
[1]1ia2.b tq420 . . . . . . . . . . . . . . . . ndp
[1]1ia3.b none . . . . . . . . . . . . . . . . ndp
[1]1m78.b clz14 . . . . . . . . . . . . . . . . ndp
[1]1m79.b mq121 . . . . . . . . . . . . . . . . ndp
[1]1m7a.b mqu22 . . . . . . . . . . . . . . . . ndp
[1]3qlr.a qlr26 . . . . . . . . . . . . . . . . ndp
[1]3qls.a 55v26 . . . . . . . . . . . . . . . . ndp
[1]3qlw.a n2223 . . . . . . . . . . . . . . . . ndp
[1]4h95.a 06u28 . . . . . . . . . . . . . . . . ndp
[1]4h96.b 14q30 . . . . . . . . . . . . . . . . ndp
[1]4h97.b 53s28 . . . . . . . . . . . . . . . . ndp
[1]4hoe.b 18g29 . . . . . . . . . . . . . . . . ndp
[1]4hof.b 18h27 . . . . . . . . . . . . . . . . ndp

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
I
9
V
1
0
A
1
1
K
2
4
M
2
5
E
3
2
I
3
3
F
3
6
K
3
7
M
5
4
T
5
8
S
6
1
I
6
2
P
6
3
F
6
6
L
6
9
P
7
0
I
1
1
2
Y
1
1
8
T
1
3
3
[1]1aoe.a . . . . . . . . . . . . . . . . . . . . ndp
[1]1ia1.b . . . . . . . . . . . . . . . . . . . . ndp
[1]1ia2.b . . . . . . . . . . . . . . . . . . . . ndp
[1]1ia3.b . . . . . . . . . . . . . . . . . . . . ndp
[1]1m78.b . . . . . . . . . . . . . . . . . . . . ndp
[1]1m79.b . . . . . . . . . . . . . . . . . . . . ndp
[1]1m7a.b . . . . . . . . . . . . . . . . . . . . ndp
[1]3qlr.a . . . . . . . . . . . * . . . . . . . . ndp
[1]3qls.a . . . . . . . . . . . * . . . . . . . . ndp
[1]3qlw.a . . . . . . . . . . . . . . . . . . . . ndp
[1]4h95.a . . . . . . . . . . . . . . . . . . . . ndp
[1]4h96.b . . . . . . . . . . . . . . . . . . . . ndp
[1]4h97.b . . . . . . . . . . . . . . . . . . . . ndp
[1]4hoe.b . . . . . . . . . . . . . . . . . . . . ndp
[1]4hof.b . . . . . . . . . . . * . . . . . . . . ndp

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
1aoe.a:gw3
1ia1.b:tq3
1ia2.b:tq4
1ia3.b is apo
1m78.b:clz
1m79.b:mq1
1m7a.b:mqu
3qlr.a:qlr
3qls.a:55v
3qlw.a:n22
4h95.a:06u
4h96.b:14q
4h97.b:53s
4hoe.b:18g
4hof.b:18h
[1] 1aoe.a
0
0.2 0.2 - 0 0.6 0 0 0 0.2 0.1 0.1 0 0.3 0
[1] 1ia1.b 0
0.1
0.1 - 0 0.4 0 0 0 0.2 0 0 0 0.3 0
[1] 1ia2.b 0 0.1
0
- 0 0.1 0 0 0 0 0 0 0 0 0
[1] 1ia3.b 0 0 0
-
0 0.3 0 0 0 0.3 0.2 0 0 0.1 0
[1] 1m78.b 0 0.1 0.1 -
0
0.7 0.1 0 0 0.3 0.1 0 0 0.4 0
[1] 1m79.b 0 0 0 - 0
0
0 0 0 0.1 0.1 0 0 0 0
[1] 1m7a.b 0 0.2 0.1 - 0 0.3
0
0.1 0 0.2 0 0 0 0 0
[1] 3qlr.a 0.1 0.1 0.4 - 0 0.8 0.1
0
0 0 0.1 0 0 0.4 0
[1] 3qls.a 0 0.3 0.6 - 0 1.3 0.1 0.3
0
0.2 0.1 0.1 0 0.6 0
[1] 3qlw.a 0.2 0.3 0.3 - 0.1 0.4 0.1 0.9 0.4
0
0.2 0.3 0.2 0.7 0.2
[1] 4h95.a 0 0.2 0.5 - 0 0.6 0 0.8 0.3 0
0.1
0.2 0.1 0.8 0.4
[1] 4h96.b 0 0.3 0.2 - 0.1 0.3 0 0.4 0 0 0.1
0
0 0.2 0.1
[1] 4h97.b 0.1 0.2 0.2 - 0 0.5 0.1 0.4 0.1 0.2 0.1 0.3
0
0.4 0
[1] 4hoe.b 0 0.3 0.2 - 0 0.5 0 0.4 0 0.2 0.3 0.1 0
0
0
[1] 4hof.b 0.1 0.4 1.2 - 0.1 1.6 0.3 0.7 0.2 0.2 0.1 0.1 0.3 0.7
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
1aoe.a
1ia1.b
1ia2.b
1ia3.b
1m78.b
1m79.b
1m7a.b
3qlr.a
3qls.a
3qlw.a
4h95.a
4h96.b
4h97.b
4hoe.b
4hof.b
[1] 1aoe.a
0
.02 .03 .03 .02 .03 .03 .02 .05 .07 .06 .04 .04 .05 .06
[1] 1ia1.b .02
0
.03 .02 .01 .03 .03 .03 .06 .07 .06 .04 .05 .05 .06
[1] 1ia2.b .03 .03
0
.03 .04 .01 .02 .04 .07 .07 .07 .03 .06 .04 .09
[1] 1ia3.b .03 .02 .03
0
.03 .03 .02 .04 .07 .06 .07 .02 .06 .04 .07
[1] 1m78.b .02 .01 .04 .03
0
.04 .02 .02 .04 .08 .06 .05 .05 .04 .04
[1] 1m79.b .03 .03 .01 .03 .04
0
.02 .04 .07 .07 .08 .04 .06 .04 .09
[1] 1m7a.b .03 .03 .02 .02 .02 .02
0
.04 .06 .07 .08 .04 .06 .02 .07
[1] 3qlr.a .02 .03 .04 .04 .02 .04 .04
0
.03 .08 .06 .05 .05 .06 .04
[1] 3qls.a .05 .06 .07 .07 .04 .07 .06 .03
0
.07 .06 .06 .06 .04 .01
[1] 3qlw.a .07 .07 .07 .06 .08 .07 .07 .08 .07
0
.03 .05 .05 .05 .08
[1] 4h95.a .06 .06 .07 .07 .06 .08 .08 .06 .06 .03
0
.05 .04 .07 .07
[1] 4h96.b .04 .04 .03 .02 .05 .04 .04 .05 .06 .05 .05
0
.05 .04 .07
[1] 4h97.b .04 .05 .06 .06 .05 .06 .06 .05 .06 .05 .04 .05
0
.06 .08
[1] 4hoe.b .05 .05 .04 .04 .04 .04 .02 .06 .04 .05 .07 .04 .06
0
.04
[1] 4hof.b .06 .06 .09 .07 .04 .09 .07 .04 .01 .08 .07 .07 .08 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1aoe.a
1ia1.b
1ia2.b
1ia3.b
1m78.b
1m79.b
1m7a.b
3qlr.a
3qls.a
3qlw.a
4h95.a
4h96.b
4h97.b
4hoe.b
4hof.b
[1] 1aoe.a
0
0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.4 0.7 0.7 0.6 0.7 0.5 0.6
[1] 1ia1.b 0.2
0
0.2 0.3 0.2 0.3 0.2 0.3 0.5 0.8 0.8 0.7 0.8 0.4 0.6
[1] 1ia2.b 0.2 0.2
0
0.2 0.3 0.2 0.3 0.3 0.5 0.7 0.8 0.7 0.7 0.5 0.6
[1] 1ia3.b 0.3 0.3 0.2
0
0.4 0.3 0.4 0.4 0.6 0.8 0.8 0.7 0.7 0.6 0.7
[1] 1m78.b 0.3 0.2 0.3 0.4
0
0.5 0.1 0.3 0.3 0.6 0.7 0.7 0.7 0.3 0.4
[1] 1m79.b 0.3 0.3 0.2 0.3 0.5
0
0.4 0.4 0.6 0.9 0.9 0.7 0.8 0.7 0.8
[1] 1m7a.b 0.3 0.2 0.3 0.4 0.1 0.4
0
0.3 0.4 0.6 0.7 0.7 0.7 0.4 0.5
[1] 3qlr.a 0.2 0.3 0.3 0.4 0.3 0.4 0.3
0
0.3 0.6 0.6 0.5 0.6 0.5 0.6
[1] 3qls.a 0.4 0.5 0.5 0.6 0.3 0.6 0.4 0.3
0
0.5 0.5 0.6 0.6 0.3 0.3
[1] 3qlw.a 0.7 0.8 0.7 0.8 0.6 0.9 0.6 0.6 0.5
0
0.2 0.6 0.4 0.6 0.6
[1] 4h95.a 0.7 0.8 0.8 0.8 0.7 0.9 0.7 0.6 0.5 0.2
0
0.6 0.4 0.7 0.6
[1] 4h96.b 0.6 0.7 0.7 0.7 0.7 0.7 0.7 0.5 0.6 0.6 0.6
0
0.5 0.8 0.9
[1] 4h97.b 0.7 0.8 0.7 0.7 0.7 0.8 0.7 0.6 0.6 0.4 0.4 0.5
0
0.8 0.8
[1] 4hoe.b 0.5 0.4 0.5 0.6 0.3 0.7 0.4 0.5 0.3 0.6 0.7 0.8 0.8
0
0.2
[1] 4hof.b 0.6 0.6 0.6 0.7 0.4 0.8 0.5 0.6 0.3 0.6 0.6 0.9 0.8 0.2
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
1aoe.a
1ia1.b
1ia2.b
1ia3.b
1m78.b
1m79.b
1m7a.b
3qlr.a
3qls.a
3qlw.a
4h95.a
4h96.b
4h97.b
4hoe.b
4hof.b
[1] 1aoe.a
0
1.1 1.1 1.1 1.1 1.1 1.2 0.6 0.6 1.3 1.2 1.2 1.3 1.2 0.9
[1] 1ia1.b 1.1
0
0.8 0.9 0.9 0.9 0.9 1.1 1.1 1.5 1.5 1.3 1.1 1.1 1.1
[1] 1ia2.b 1.1 0.8
0
0.4 0.4 0.3 0.3 0.9 1.1 1.2 1.3 1.0 1.3 0.7 1.0
[1] 1ia3.b 1.1 0.9 0.4
0
0.5 0.4 0.5 0.9 1.1 1.2 1.3 1.0 1.3 0.8 1.0
[1] 1m78.b 1.1 0.9 0.4 0.5
0
0.6 0.3 0.9 1.0 1.1 1.2 0.9 1.2 0.7 0.8
[1] 1m79.b 1.1 0.9 0.3 0.4 0.6
0
0.5 1.0 1.2 1.3 1.4 1.0 1.3 0.8 1.1
[1] 1m7a.b 1.2 0.9 0.3 0.5 0.3 0.5
0
1.0 1.1 1.1 1.2 0.9 1.2 0.7 0.8
[1] 3qlr.a 0.6 1.1 0.9 0.9 0.9 1.0 1.0
0
0.5 1.1 1.0 0.9 1.2 0.9 0.7
[1] 3qls.a 0.6 1.1 1.1 1.1 1.0 1.2 1.1 0.5
0
1.0 1.0 1.1 1.2 1.0 0.7
[1] 3qlw.a 1.3 1.5 1.2 1.2 1.1 1.3 1.1 1.1 1.0
0
0.6 0.9 1.1 1.0 0.9
[1] 4h95.a 1.2 1.5 1.3 1.3 1.2 1.4 1.2 1.0 1.0 0.6
0
0.9 1.0 1.2 1.0
[1] 4h96.b 1.2 1.3 1.0 1.0 0.9 1.0 0.9 0.9 1.1 0.9 0.9
0
1.0 1.0 1.0
[1] 4h97.b 1.3 1.1 1.3 1.3 1.2 1.3 1.2 1.2 1.2 1.1 1.0 1.0
0
1.2 1.2
[1] 4hoe.b 1.2 1.1 0.7 0.8 0.7 0.8 0.7 0.9 1.0 1.0 1.2 1.0 1.2
0
0.6
[1] 4hof.b 0.9 1.1 1.0 1.0 0.8 1.1 0.8 0.7 0.7 0.9 1.0 1.0 1.2 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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