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HGF_HUMAN_126_210

Hepatocyte growth factor [Peptidase S1 family. Plasminogen subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (HGF_HUMAN):D: Kringle 1 (162, 181, 183, 188, 190, 197, 198)162, 181, 183, 188, 190, 197, 198

Full PDB list

1bht, 1gmn, 1gmo, 1gp9, 1nk1, 2qj2, 3hn4, 3mkp, 3sp8, 4d3c, 5coe, 5cp9, 5cs1, 5cs3, 5cs5, 5cs9, 5csq, 5ct1, 5ct2, 5ct3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
6
2
R
1
8
1
E
1
8
3
W
1
8
8
F
1
9
0
R
1
9
7
Y
1
9
8
[1]2qj2.a none . . . . . . .
[1]4d3c.a T7 . . . . . . .
[1]5cp9.b 6o510 . . . . . . .
[1]5ct3.b 54o8 . . . . . . .

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

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PDB.ch
A1
F
1
6
2
R
1
8
1
E
1
8
3
W
1
8
8
F
1
9
0
R
1
9
7
Y
1
9
8
[1]2qj2.a . . . . . . .
[1]4d3c.a . . . . . . .
[1]5cp9.b . . . . . . .
[1]5ct3.b . . . . . . .

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
2qj2.a is apo
4d3c.a:T
5cp9.b:6o5
5ct3.b:54o
[1] 2qj2.a
-
0.5 0.3 0
[1] 4d3c.a -
0
0.4 0.3
[1] 5cp9.b - 0.3
0
0
[1] 5ct3.b - 0.5 0.2
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
2qj2.a
4d3c.a
5cp9.b
5ct3.b
[1] 2qj2.a
0
.10 .04 .01
[1] 4d3c.a .10
0
.09 .11
[1] 5cp9.b .04 .09
0
.02
[1] 5ct3.b .01 .11 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2qj2.a
4d3c.a
5cp9.b
5ct3.b
[1] 2qj2.a
0
0.7 0.4 0.4
[1] 4d3c.a 0.7
0
0.6 0.6
[1] 5cp9.b 0.4 0.6
0
0.1
[1] 5ct3.b 0.4 0.6 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2qj2.a
4d3c.a
5cp9.b
5ct3.b
[1] 2qj2.a
0
1.3 0.9 0.8
[1] 4d3c.a 1.3
0
1.4 1.4
[1] 5cp9.b 0.9 1.4
0
0.5
[1] 5ct3.b 0.8 1.4 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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