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DRTS_TRYCR_1_521

Bifunctional dihydrofolate reductase-thymidylate synthase

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DRTS_TRYCR):D: DHFR (26:28, 35:41, 43:45, 48, 49, 52, 53, 77:80, 83:85, 88, 91, 92, 94, 99:103, 129:131, 154:160, 178, 189)
R: Thymidylate synthase (256:258, 262, 343, 390, 400:405, 422:426, 429, 430, 434, 438, 464, 466)
26:28, 35:41, 43:45, 48, 49, 52, 53, 77:80, 83:85, 88, 91, 92, 94, 99:103, 129:131, 154:160, 178, 189, 256:258, 262, 343, 390, 400:405, 422:426, 429, 430, 434, 438, 464, 466

Full PDB list

2h2q, 3cl9, 3clb, 3hbb, 3inv, 3irm, 3irn, 3iro, 3kjs, 5t7o (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
2
6
V
2
7
A
2
8
I
3
5
G
3
6
D
3
7
G
3
8
R
3
9
S
4
0
I
4
1
W
4
3
N
4
4
V
4
5
D
4
8
M
4
9
F
5
2
R
5
3
G
7
7
R
7
8
K
7
9
T
8
0
S
8
3
I
8
4
P
8
5
F
8
8
L
9
1
P
9
2
R
9
4
L
9
9
S
1
0
0
S
1
0
1
T
1
0
2
N
1
2
9
G
1
3
0
G
1
3
1
I
1
5
4
G
1
5
5
G
1
5
6
G
1
5
7
S
1
5
8
V
1
5
9
Y
1
6
0
T
1
7
8
R
2
5
7
C
4
0
3
H
4
0
4
Q
4
2
2
R
4
2
3
S
4
2
4
D
4
2
6
G
4
3
0
N
4
3
4
H
4
6
4
Y
4
6
6
[1]2h2q.a nap-du68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3clb.d nap,tmq75 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3inv.b c50,ndp.ump91 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3irm.d 1cy17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3irn.c 1cy,ndp65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3iro.b 2cy,ndp72 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3kjs.c dq1,nap79 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5t7o.b nap,thg.ump100 . . . . . - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . .
[1]5t7o.d nap.ump,thg100 . . . . . - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . .
[2]3cl9.a mtx.ump,nap101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
V
2
6
V
2
7
A
2
8
I
3
5
G
3
6
D
3
7
G
3
8
R
3
9
S
4
0
I
4
1
W
4
3
N
4
4
V
4
5
D
4
8
M
4
9
F
5
2
R
5
3
G
7
7
R
7
8
K
7
9
T
8
0
S
8
3
I
8
4
P
8
5
F
8
8
L
9
1
P
9
2
R
9
4
L
9
9
S
1
0
0
S
1
0
1
T
1
0
2
L
1
0
3
N
1
2
9
G
1
3
0
G
1
3
1
I
1
5
4
G
1
5
5
G
1
5
6
G
1
5
7
S
1
5
8
V
1
5
9
Y
1
6
0
T
1
7
8
V
1
8
9
D
2
5
6
R
2
5
7
T
2
5
8
T
2
6
2
Y
3
4
3
W
3
9
0
L
4
0
0
P
4
0
1
P
4
0
2
C
4
0
3
H
4
0
4
L
4
0
5
Q
4
2
2
R
4
2
3
S
4
2
4
C
4
2
5
D
4
2
6
L
4
2
9
G
4
3
0
N
4
3
4
Y
4
3
8
H
4
6
4
Y
4
6
6
[1]2h2q.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . . . . . . . . *
[1]3clb.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * * . . * . . . . . . . . .
[1]3inv.b . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * * . . * . . . . . . . . .
[1]3irm.d . . . . . * * * . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . * * . . . . . . . . .
[1]3irn.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . * . . . . . . . . .
[1]3iro.b . . . . . . . . . * . . . . . . * . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * * . . * . . . . . . . . .
[1]3kjs.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . * . . . . . . . . .
[1]5t7o.b . . . . . - - - - - . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . - . . . . . . . * * . . * . . . . . . . . .
[1]5t7o.d . . . . . - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . * * . * * . . . . . . . . .
[2]3cl9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . . *

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
2h2q.a:nap-du
3clb.d:nap,tmq
3inv.b:c50,ndp.ump
3irm.d:1cy
3irn.c:1cy,ndp
3iro.b:2cy,ndp
3kjs.c:dq1,nap
5t7o.b:nap,thg.ump
5t7o.d:nap.ump,thg
3cl9.a:mtx.ump,nap
[1] 2h2q.a
0.4
0.4 2.5 0.3 1.6 1.0 0.4 2.2 2.2 8.6
[1] 3clb.d 0.8
0.2
2.2 0.4 1.6 1.1 1.0 1.4 1.9 9.7
[1] 3inv.b 4.6 0.7
0.2
0.3 0.9 0.6 0.3 5.4 5.3 15
[1] 3irm.d 5.4 3.8 4.5
0.1
4.2 3.4 4.9 4.7 5.5 15
[1] 3irn.c 1.0 0.3 1.7 0
0.2
0.5 1.5 1.5 1.4 11
[1] 3iro.b 2.3 0.9 1.6 0.1 0.9
0.2
2.5 3.7 4.1 14
[1] 3kjs.c 0.5 0.3 1.1 0.6 1.1 1.1
0.1
1.7 1.9 8.9
[1] 5t7o.b 1.5 1.4 1.6 0.6 1.5 0.9 1.0
0.8
0.9 11
[1] 5t7o.d 1.9 1.1 1.3 0.4 0.9 0.7 1.1 0.5
0.4
12
[2] 3cl9.a 4.6 1.8 10 0.7 1.5 2.6 1.4 8.2 8.2
0.5
[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
2h2q.a
3clb.d
3inv.b
3irm.d
3irn.c
3iro.b
3kjs.c
5t7o.b
5t7o.d
3cl9.a
[1] 2h2q.a
0
.07 .20 .20 .11 .17 .10 .11 .12 .25
[1] 3clb.d .07
0
.17 .17 .10 .15 .07 .10 .12 .28
[1] 3inv.b .20 .17
0
.21 .17 .13 .15 .14 .14 .38
[1] 3irm.d .20 .17 .21
0
.15 .18 .17 .14 .13 .41
[1] 3irn.c .11 .10 .17 .15
0
.12 .10 .10 .10 .30
[1] 3iro.b .17 .15 .13 .18 .12
0
.16 .11 .12 .38
[1] 3kjs.c .10 .07 .15 .17 .10 .16
0
.09 .11 .27
[1] 5t7o.b .11 .10 .14 .14 .10 .11 .09
0
.03 .32
[1] 5t7o.d .12 .12 .14 .13 .10 .12 .11 .03
0
.33
[2] 3cl9.a .25 .28 .38 .41 .30 .38 .27 .32 .33
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
2h2q.a
3clb.d
3inv.b
3irm.d
3irn.c
3iro.b
3kjs.c
5t7o.b
5t7o.d
3cl9.a
[1] 2h2q.a
0
0.6 2.0 1.6 1.1 1.4 0.8 1.3 1.3 2.1
[1] 3clb.d 0.6
0
1.8 1.5 1.0 1.4 0.5 1.1 1.1 2.4
[1] 3inv.b 2.0 1.8
0
1.2 1.4 1.1 1.8 1.2 1.1 3.9
[1] 3irm.d 1.6 1.5 1.2
0
1.1 0.8 1.5 0.7 0.6 3.4
[1] 3irn.c 1.1 1.0 1.4 1.1
0
0.9 1.1 0.9 0.8 2.7
[1] 3iro.b 1.4 1.4 1.1 0.8 0.9
0
1.5 0.7 0.5 3.3
[1] 3kjs.c 0.8 0.5 1.8 1.5 1.1 1.5
0
1.2 1.3 2.5
[1] 5t7o.b 1.3 1.1 1.2 0.7 0.9 0.7 1.2
0
0.3 3.1
[1] 5t7o.d 1.3 1.1 1.1 0.6 0.8 0.5 1.3 0.3
0
3.1
[2] 3cl9.a 2.1 2.4 3.9 3.4 2.7 3.3 2.5 3.1 3.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
2h2q.a
3clb.d
3inv.b
3irm.d
3irn.c
3iro.b
3kjs.c
5t7o.b
5t7o.d
3cl9.a
[1] 2h2q.a
0
0.9 2.3 1.9 1.5 1.8 1.2 1.4 1.4 2.4
[1] 3clb.d 0.9
0
2.1 1.8 1.4 1.7 0.9 1.4 1.3 2.6
[1] 3inv.b 2.3 2.1
0
1.7 1.8 1.3 2.1 1.5 1.4 4.3
[1] 3irm.d 1.9 1.8 1.7
0
1.6 1.3 2.0 1.0 0.9 3.7
[1] 3irn.c 1.5 1.4 1.8 1.6
0
1.4 1.5 1.2 1.1 3.1
[1] 3iro.b 1.8 1.7 1.3 1.3 1.4
0
1.9 1.1 1.0 3.6
[1] 3kjs.c 1.2 0.9 2.1 2.0 1.5 1.9
0
1.4 1.4 2.8
[1] 5t7o.b 1.4 1.4 1.5 1.0 1.2 1.1 1.4
0
0.4 3.3
[1] 5t7o.d 1.4 1.3 1.4 0.9 1.1 1.0 1.4 0.4
0
3.3
[2] 3cl9.a 2.4 2.6 4.3 3.7 3.1 3.6 2.8 3.3 3.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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