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CXCR4_HUMAN_1_319_TM

C-X-C chemokine receptor type 4 [G-protein coupled receptor 1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CXCR4_HUMAN):R: Chemokine binding (94, 97)
R: Chemokine binding (113, 116, 117)
R: Chemokine binding, important for signaling and HIV-1 coreceptor activity (186:190)
R: Involved in dimerization (191:193, 196, 197, 199:201, 203:205, 209)
R: Involved in dimerization (266, 267)
25:27, 30, 32, 37, 98, 102, 112, 171, 178, 183, 185, 259, 262:265, 280, 281, 284, 285, 288
25:27, 30, 32, 37, 94, 97, 98, 102, 112, 113, 116, 117, 171, 178, 183, 185:193, 196, 197, 199:201, 203:205, 209, 259, 262:267, 280, 281, 284, 285, 288

Full PDB list

3odu, 3oe0, 3oe6, 3oe8, 3oe9, 4rws (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
P
2
7
E
3
2
W
9
4
D
9
7
A
9
8
W
1
0
2
V
1
1
2
H
1
1
3
Y
1
1
6
T
1
1
7
D
1
7
1
R
1
8
3
I
1
8
5
C
1
8
6
D
1
8
7
R
1
8
8
F
1
8
9
Y
1
9
0
P
1
9
1
N
1
9
2
D
1
9
3
V
1
9
6
V
1
9
7
F
1
9
9
Q
2
0
0
F
2
0
1
I
2
0
4
I
2
0
9
I
2
5
9
D
2
6
2
S
2
6
3
L
2
6
6
H
2
8
1
I
2
8
4
S
2
8
5
E
2
8
8
[1]3odu.a itd,olc49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3odu.b itd,ola47 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3oe0.a RRalnCYQKdprPYRcirCRGdpr150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3oe8.a itd27 . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4rws.a LGASCH-QL-P63 . . . . . . . . . . . . . . C . . . . . . . . . . . . . . . . . . . . .

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
K
2
5
E
2
6
P
2
7
R
3
0
E
3
2
N
3
7
W
9
4
D
9
7
A
9
8
W
1
0
2
V
1
1
2
H
1
1
3
Y
1
1
6
T
1
1
7
D
1
7
1
S
1
7
8
R
1
8
3
I
1
8
5
C
1
8
6
D
1
8
7
R
1
8
8
F
1
8
9
Y
1
9
0
P
1
9
1
N
1
9
2
D
1
9
3
V
1
9
6
V
1
9
7
F
1
9
9
Q
2
0
0
F
2
0
1
H
2
0
3
I
2
0
4
M
2
0
5
I
2
0
9
I
2
5
9
D
2
6
2
S
2
6
3
F
2
6
4
I
2
6
5
L
2
6
6
L
2
6
7
V
2
8
0
H
2
8
1
I
2
8
4
S
2
8
5
E
2
8
8
[1]3odu.a - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]3odu.b - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . . .
[1]3oe0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . * * . . . . . * . . .
[1]3oe8.a - - . - - . . . . . . . . . . . . . . . . . . . . * . . . * * . . . . . * * . . . . . . . . .
[1]4rws.a . . . . . . . . . . . . . . . . * . . C . . . . . . . . . * . . . . . . . . . . * . . . . . .

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
3odu.a:itd,olc
3odu.b:itd,ola
3oe0.a:RRalnCYQKdprPYRcirCRGdpr
3oe8.a:itd
4rws.a:LGASCH-QL-P
[1] 3odu.a
0
0 6.0 0.1 2.2
[1] 3odu.b 0
0
6.1 0 4.1
[1] 3oe0.a 3.4 3.6
0
0.9 3.0
[1] 3oe8.a 6.5 6.7 5.1
0
1.8
[1] 4rws.a 3.9 3.6 3.5 2.2
0.4
[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
3odu.a
3odu.b
3oe0.a
3oe8.a
4rws.a
[1] 3odu.a
0
.07 .20 .21 .20
[1] 3odu.b .07
0
.20 .24 .25
[1] 3oe0.a .20 .20
0
.23 .22
[1] 3oe8.a .21 .24 .23
0
.31
[1] 4rws.a .20 .25 .22 .31
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
3odu.a
3odu.b
3oe0.a
3oe8.a
4rws.a
[1] 3odu.a
0
0.3 1.8 1.6 2.2
[1] 3odu.b 0.3
0
1.6 1.5 2.0
[1] 3oe0.a 1.8 1.6
0
1.2 3.9
[1] 3oe8.a 1.6 1.5 1.2
0
2.6
[1] 4rws.a 2.2 2.0 3.9 2.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.6 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
3odu.a
3odu.b
3oe0.a
3oe8.a
4rws.a
[1] 3odu.a
0
1.3 2.4 1.9 2.6
[1] 3odu.b 1.3
0
2.4 1.9 2.7
[1] 3oe0.a 2.4 2.4
0
1.9 4.2
[1] 3oe8.a 1.9 1.9 1.9
0
2.8
[1] 4rws.a 2.6 2.7 4.2 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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