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Fluorine in PDB 4jp4: MMP13 in Complex with A Reverse Hydroxamate Zn-Binder

Protein crystallography data

The structure of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder, PDB code: 4jp4 was solved by S.Gerhardt, D.Hargreaves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.16 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.616, 36.130, 95.755, 90.00, 131.02, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 4jp4:

The structure of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Calcium (Ca) 4 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder (pdb code 4jp4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder, PDB code: 4jp4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 1 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F306

b:11.2
occ:1.00
 F1 A:AZ4306 0.0 11.2 1.0
C7 A:AZ4306 1.4 10.0 1.0
C8 A:AZ4306 2.4 9.3 1.0
C6 A:AZ4306 2.4 8.5 1.0
ND1 A:HIS226 3.1 6.2 1.0
CE1 A:HIS226 3.3 6.3 1.0
CG A:HIS226 3.3 5.2 1.0
CZ B:PHE107 3.5 14.8 1.0
NE2 A:HIS226 3.6 5.9 1.0
N3 A:AZ4306 3.6 9.3 1.0
N2 A:AZ4306 3.6 8.9 1.0
CD2 A:HIS226 3.6 6.2 1.0
CE1 B:PHE107 3.8 14.7 1.0
CB A:HIS226 4.0 5.6 1.0
C5 A:AZ4306 4.0 7.8 1.0
OD1 A:ASP231 4.1 10.4 1.0
O A:ALA188 4.2 8.2 1.0
O A:HOH642 4.3 25.1 1.0
CE2 B:PHE107 4.6 16.2 1.0
O A:LEU230 4.8 7.1 1.0
CG A:ASP231 4.8 9.4 1.0
CA A:ASP231 4.9 7.2 1.0
CA A:HIS226 5.0 5.2 1.0

Fluorine binding site 2 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 2 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F306

b:22.4
occ:1.00
 F2 A:AZ4306 0.0 22.4 1.0
C18 A:AZ4306 1.4 19.4 1.0
F4 A:AZ4306 2.2 15.6 1.0
F3 A:AZ4306 2.2 21.4 1.0
C17 A:AZ4306 2.4 16.1 1.0
O5 A:AZ4306 2.8 11.8 1.0
O A:THR245 3.1 25.1 1.0
O A:HOH648 3.8 39.2 1.0
C16 A:AZ4306 4.0 9.0 1.0
CD2 A:LEU218 4.1 13.3 1.0
CD1 A:LEU218 4.2 12.8 1.0
C A:THR245 4.3 23.7 1.0
O A:HOH624 4.4 23.9 1.0
O A:HOH627 4.5 26.5 1.0
CG A:LEU218 4.6 12.5 1.0
OG1 A:THR245 4.7 25.3 1.0
C15 A:AZ4306 4.7 8.9 1.0
C19 A:AZ4306 4.8 8.1 1.0
N A:THR245 4.8 20.9 1.0
CB A:LEU218 4.9 9.1 1.0
CD1 A:LEU239 4.9 7.0 1.0
CE2 A:PHE252 4.9 17.4 1.0
O A:HOH618 4.9 16.0 1.0

Fluorine binding site 3 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 3 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F306

b:21.4
occ:1.00
 F3 A:AZ4306 0.0 21.4 1.0
C18 A:AZ4306 1.4 19.4 1.0
F4 A:AZ4306 2.2 15.6 1.0
F2 A:AZ4306 2.2 22.4 1.0
C17 A:AZ4306 2.4 16.1 1.0
O A:HOH627 2.8 26.5 1.0
O A:HOH618 3.0 16.0 1.0
O5 A:AZ4306 3.5 11.8 1.0
O A:HOH624 3.7 23.9 1.0
O A:ALA238 3.8 8.1 1.0
C A:ALA238 4.3 8.8 1.0
O A:HOH597 4.3 38.3 1.0
CA A:LEU239 4.4 6.7 1.0
O A:GLY237 4.4 12.7 1.0
O A:THR245 4.4 25.1 1.0
OG1 A:THR245 4.5 25.3 1.0
N A:LEU239 4.6 7.6 1.0
C16 A:AZ4306 4.7 9.0 1.0
C A:GLY237 4.9 11.7 1.0
O A:HOH648 4.9 39.2 1.0
C15 A:AZ4306 5.0 8.9 1.0

Fluorine binding site 4 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 4 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F306

b:15.6
occ:1.00
 F4 A:AZ4306 0.0 15.6 1.0
C18 A:AZ4306 1.4 19.4 1.0
F2 A:AZ4306 2.2 22.4 1.0
F3 A:AZ4306 2.2 21.4 1.0
C17 A:AZ4306 2.4 16.1 1.0
O5 A:AZ4306 2.7 11.8 1.0
CD1 A:LEU239 3.2 7.0 1.0
CA A:LEU239 3.5 6.7 1.0
CE2 A:PHE252 3.6 17.4 1.0
CB A:LEU239 4.0 6.4 1.0
C16 A:AZ4306 4.0 9.0 1.0
CG A:LEU239 4.2 6.3 1.0
N A:LEU239 4.3 7.6 1.0
CZ A:PHE252 4.4 16.1 1.0
CD2 A:LEU218 4.4 13.3 1.0
O A:ALA238 4.4 8.1 1.0
O A:LEU239 4.4 6.2 1.0
C A:LEU239 4.5 6.9 1.0
CD2 A:PHE252 4.6 18.7 1.0
C A:ALA238 4.7 8.8 1.0
O A:HOH648 4.7 39.2 1.0
O A:HOH597 4.7 38.3 1.0
O A:HOH618 4.8 16.0 1.0
C15 A:AZ4306 4.9 8.9 1.0
O A:HOH627 4.9 26.5 1.0
C19 A:AZ4306 4.9 8.1 1.0

Fluorine binding site 5 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 5 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:9.7
occ:1.00
 F1 B:AZ4306 0.0 9.7 1.0
C7 B:AZ4306 1.3 7.2 1.0
C8 B:AZ4306 2.4 9.2 1.0
C6 B:AZ4306 2.4 7.2 1.0
ND1 B:HIS226 3.0 6.3 1.0
CE1 B:HIS226 3.2 8.1 1.0
CG B:HIS226 3.3 5.3 1.0
CZ A:PHE107 3.3 14.3 1.0
CE2 A:PHE107 3.5 13.5 1.0
NE2 B:HIS226 3.5 7.2 1.0
CD2 B:HIS226 3.5 6.6 1.0
N2 B:AZ4306 3.6 7.5 1.0
N3 B:AZ4306 3.6 7.0 1.0
CB B:HIS226 3.9 7.0 1.0
C5 B:AZ4306 4.0 7.5 1.0
O B:HOH606 4.2 32.3 1.0
OD1 B:ASP231 4.3 12.4 1.0
O B:ALA188 4.3 8.5 1.0
O B:HOH600 4.3 20.6 1.0
CE1 A:PHE107 4.6 13.7 1.0
O B:LEU230 4.8 8.4 1.0
CD2 A:PHE107 4.8 14.2 1.0
O B:HOH624 4.9 28.9 1.0
CA B:HIS226 4.9 6.6 1.0

Fluorine binding site 6 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 6 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:15.4
occ:1.00
 F2 B:AZ4306 0.0 15.4 1.0
C18 B:AZ4306 1.4 13.4 1.0
F4 B:AZ4306 2.2 10.7 1.0
F3 B:AZ4306 2.2 15.0 1.0
C17 B:AZ4306 2.4 9.7 1.0
O5 B:AZ4306 2.8 9.7 1.0
O B:THR245 3.1 8.9 1.0
O B:HOH593 3.2 12.9 1.0
O B:HOH627 3.7 10.0 1.0
OG1 B:THR245 3.7 8.7 1.0
C16 B:AZ4306 4.0 6.5 1.0
C B:THR245 4.0 8.6 1.0
CD2 B:LEU218 4.1 11.1 1.0
N B:THR245 4.1 8.3 1.0
CD1 B:LEU218 4.3 10.3 1.0
O B:HOH608 4.4 40.3 1.0
CA B:THR245 4.5 7.9 1.0
O B:HOH590 4.6 10.0 1.0
CG B:LEU218 4.7 9.9 1.0
C15 B:AZ4306 4.7 7.7 1.0
CB B:THR245 4.8 8.6 1.0
O B:HOH628 4.8 23.9 1.0
C19 B:AZ4306 4.8 7.1 1.0

Fluorine binding site 7 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 7 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:15.0
occ:1.00
 F3 B:AZ4306 0.0 15.0 1.0
C18 B:AZ4306 1.3 13.4 1.0
F4 B:AZ4306 2.2 10.7 1.0
F2 B:AZ4306 2.2 15.4 1.0
C17 B:AZ4306 2.4 9.7 1.0
O B:HOH608 3.0 40.3 1.0
O B:HOH586 3.1 10.3 1.0
O B:HOH590 3.5 10.0 1.0
O5 B:AZ4306 3.5 9.7 1.0
O B:HOH628 3.7 23.9 1.0
OG1 B:THR245 3.7 8.7 1.0
O B:HOH627 3.8 10.0 1.0
O B:ALA238 3.9 8.6 1.0
C B:ALA238 4.6 8.1 1.0
O B:HOH593 4.6 12.9 1.0
O B:GLY237 4.6 10.1 1.0
CA B:LEU239 4.6 7.4 1.0
C16 B:AZ4306 4.7 6.5 1.0
O B:THR245 4.8 8.9 1.0
N B:LEU239 4.8 7.4 1.0
O B:ILE243 4.9 8.6 1.0
C15 B:AZ4306 5.0 7.7 1.0

Fluorine binding site 8 out of 8 in 4jp4

Go back to Fluorine Binding Sites List in 4jp4
Fluorine binding site 8 out of 8 in the MMP13 in Complex with A Reverse Hydroxamate Zn-Binder


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of MMP13 in Complex with A Reverse Hydroxamate Zn-Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F306

b:10.7
occ:1.00
 F4 B:AZ4306 0.0 10.7 1.0
C18 B:AZ4306 1.4 13.4 1.0
F3 B:AZ4306 2.2 15.0 1.0
F2 B:AZ4306 2.2 15.4 1.0
C17 B:AZ4306 2.4 9.7 1.0
O5 B:AZ4306 2.7 9.7 1.0
O B:HOH608 3.3 40.3 1.0
CD1 B:LEU239 3.5 7.6 1.0
CA B:LEU239 3.6 7.4 1.0
CE2 B:PHE252 3.8 13.4 1.0
C16 B:AZ4306 4.1 6.5 1.0
CB B:LEU239 4.1 7.0 1.0
N B:LEU239 4.2 7.4 1.0
CZ B:PHE252 4.3 11.1 1.0
CD2 B:LEU218 4.3 11.1 1.0
O B:ALA238 4.4 8.6 1.0
CG B:LEU239 4.4 6.9 1.0
O B:LEU239 4.6 7.1 1.0
C B:LEU239 4.6 6.7 1.0
C B:ALA238 4.6 8.1 1.0
O B:HOH593 4.6 12.9 1.0
O B:HOH586 4.8 10.3 1.0
C15 B:AZ4306 4.9 7.7 1.0
CD2 B:PHE252 5.0 12.9 1.0

Reference:

C.De Savi, D.Waterson, A.Pape, S.Lamont, E.Hadley, M.Mills, K.M.Page, J.Bowyer, R.A.Maciewicz. Hydantoin Based Inhibitors of MMP13--Discovery of AZD6605. Bioorg.Med.Chem.Lett. V. 23 4705 2013.
ISSN: ISSN 0960-894X
PubMed: 23810497
DOI: 10.1016/J.BMCL.2013.05.089
Page generated: Mon Jul 14 22:38:49 2025

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