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Fluorine in PDB 3kry: Crystal Structure of Mmp-13 in Complex with Sc-78080

Protein crystallography data

The structure of Crystal Structure of Mmp-13 in Complex with Sc-78080, PDB code: 3kry was solved by J.R.Kiefer, J.M.Williams, D.P.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.68 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.317, 70.016, 69.094, 92.42, 94.23, 104.94
R / Rfree (%) 20.6 / 25.6

Other elements in 3kry:

The structure of Crystal Structure of Mmp-13 in Complex with Sc-78080 also contains other interesting chemical elements:

Calcium (Ca) 8 atoms
Zinc (Zn) 8 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Mmp-13 in Complex with Sc-78080 (pdb code 3kry). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Mmp-13 in Complex with Sc-78080, PDB code: 3kry:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 3kry

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Fluorine binding site 1 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1800

b:23.5
occ:1.00
 F33 A:3KR1800 0.0 23.5 1.0
C32 A:3KR1800 1.3 21.7 1.0
F35 A:3KR1800 2.2 21.8 1.0
F34 A:3KR1800 2.2 22.5 1.0
O31 A:3KR1800 2.3 19.8 1.0
C28 A:3KR1800 2.9 17.7 1.0
C29 A:3KR1800 3.2 17.5 1.0
O A:THR245 3.7 16.1 1.0
CG2 A:THR247 4.0 23.3 1.0
CD2 A:LEU218 4.0 7.3 1.0
C27 A:3KR1800 4.0 16.1 1.0
CD1 A:LEU239 4.2 9.6 1.0
CD1 A:LEU218 4.3 5.5 1.0
OG1 A:THR245 4.3 15.6 1.0
C30 A:3KR1800 4.4 17.2 1.0
CE1 A:PHE252 4.4 21.9 1.0
CG A:LEU218 4.4 6.8 1.0
CB A:LEU218 4.5 6.5 1.0
C A:THR245 4.8 16.0 1.0
O A:HOH3 4.9 7.9 1.0
C26 A:3KR1800 5.0 15.9 1.0

Fluorine binding site 2 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 2 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1800

b:22.5
occ:1.00
 F34 A:3KR1800 0.0 22.5 1.0
C32 A:3KR1800 1.3 21.7 1.0
F33 A:3KR1800 2.2 23.5 1.0
F35 A:3KR1800 2.2 21.8 1.0
O31 A:3KR1800 2.3 19.8 1.0
C28 A:3KR1800 3.0 17.7 1.0
O A:HOH3 3.2 7.9 1.0
CA A:LEU239 3.4 9.8 1.0
C27 A:3KR1800 3.4 16.1 1.0
O A:ALA238 3.6 10.5 1.0
N A:LEU239 3.8 10.5 1.0
C A:ALA238 3.9 10.4 1.0
CD1 A:LEU239 4.0 9.6 1.0
C29 A:3KR1800 4.0 17.5 1.0
CB A:LEU239 4.2 10.1 1.0
C A:LEU239 4.3 9.9 1.0
O A:LEU239 4.3 9.9 1.0
O A:HOH25 4.5 2.0 1.0
OG1 A:THR245 4.6 15.6 1.0
C26 A:3KR1800 4.6 15.9 1.0
O A:GLY237 4.7 10.5 1.0
CG A:LEU239 4.7 10.1 1.0

Fluorine binding site 3 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 3 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1800

b:21.8
occ:1.00
 F35 A:3KR1800 0.0 21.8 1.0
C32 A:3KR1800 1.3 21.7 1.0
F33 A:3KR1800 2.2 23.5 1.0
F34 A:3KR1800 2.2 22.5 1.0
O31 A:3KR1800 2.3 19.8 1.0
OG1 A:THR245 2.9 15.6 1.0
O A:HOH3 3.5 7.9 1.0
C28 A:3KR1800 3.6 17.7 1.0
O A:THR245 3.8 16.1 1.0
O A:HOH25 4.1 2.0 1.0
CB A:THR245 4.3 15.0 1.0
CG2 A:THR247 4.3 23.3 1.0
C29 A:3KR1800 4.4 17.5 1.0
C A:THR245 4.5 16.0 1.0
C27 A:3KR1800 4.5 16.1 1.0
CA A:THR245 4.8 14.8 1.0
N A:THR245 4.8 13.2 1.0

Fluorine binding site 4 out of 12 in 3kry

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Fluorine binding site 4 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2800

b:21.8
occ:1.00
 F33 B:3KR2800 0.0 21.8 1.0
C32 B:3KR2800 1.3 20.2 1.0
F35 B:3KR2800 2.2 21.6 1.0
F34 B:3KR2800 2.2 23.7 1.0
O31 B:3KR2800 2.3 18.7 1.0
C28 B:3KR2800 2.9 17.8 1.0
C29 B:3KR2800 3.2 16.2 1.0
OG1 B:THR247 3.5 34.0 1.0
O B:THR245 3.6 24.8 1.0
CD2 B:LEU218 3.7 16.4 1.0
C27 B:3KR2800 4.0 15.2 1.0
CD1 B:LEU239 4.1 15.5 1.0
CE1 B:PHE252 4.1 32.6 1.0
CD1 B:LEU218 4.4 16.1 1.0
C30 B:3KR2800 4.4 16.4 1.0
OG1 B:THR245 4.4 24.7 1.0
CG B:LEU218 4.4 15.2 1.0
CB B:LEU218 4.6 14.2 1.0
CZ B:PHE252 4.7 32.2 1.0
C B:THR245 4.8 24.9 1.0
CB B:THR247 4.9 33.4 1.0

Fluorine binding site 5 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 5 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2800

b:23.7
occ:1.00
 F34 B:3KR2800 0.0 23.7 1.0
C32 B:3KR2800 1.3 20.2 1.0
F33 B:3KR2800 2.2 21.8 1.0
F35 B:3KR2800 2.2 21.6 1.0
O31 B:3KR2800 2.3 18.7 1.0
C28 B:3KR2800 2.9 17.8 1.0
C27 B:3KR2800 3.2 15.2 1.0
O B:HOH87 3.3 19.0 1.0
CA B:LEU239 3.3 17.1 1.0
O B:ALA238 3.6 17.1 1.0
CD1 B:LEU239 3.8 15.5 1.0
N B:LEU239 3.9 17.6 1.0
C29 B:3KR2800 3.9 16.2 1.0
C B:ALA238 4.0 17.8 1.0
CB B:LEU239 4.1 17.3 1.0
O B:LEU239 4.2 17.3 1.0
C B:LEU239 4.2 17.1 1.0
C26 B:3KR2800 4.4 15.5 1.0
CG B:LEU239 4.6 16.9 1.0
O B:HOH314 4.6 20.8 1.0
OG1 B:THR245 4.8 24.7 1.0
C30 B:3KR2800 4.9 16.4 1.0
O B:GLY237 4.9 19.5 1.0
CE1 B:PHE252 5.0 32.6 1.0

Fluorine binding site 6 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 6 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2800

b:21.6
occ:1.00
 F35 B:3KR2800 0.0 21.6 1.0
C32 B:3KR2800 1.3 20.2 1.0
F33 B:3KR2800 2.2 21.8 1.0
F34 B:3KR2800 2.2 23.7 1.0
O31 B:3KR2800 2.3 18.7 1.0
OG1 B:THR245 3.0 24.7 1.0
O B:HOH87 3.5 19.0 1.0
C28 B:3KR2800 3.5 17.8 1.0
O B:THR245 3.8 24.8 1.0
OG1 B:THR247 3.8 34.0 1.0
O B:HOH314 4.1 20.8 1.0
C29 B:3KR2800 4.4 16.2 1.0
CB B:THR245 4.4 24.0 1.0
C27 B:3KR2800 4.4 15.2 1.0
C B:THR245 4.6 24.9 1.0
CA B:THR245 4.9 23.7 1.0
N B:THR245 4.9 22.2 1.0

Fluorine binding site 7 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 7 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3800

b:21.6
occ:1.00
 F33 C:3KR3800 0.0 21.6 1.0
C32 C:3KR3800 1.3 22.0 1.0
F35 C:3KR3800 2.2 21.5 1.0
O31 C:3KR3800 2.2 21.1 1.0
F34 C:3KR3800 2.2 23.9 1.0
C28 C:3KR3800 2.9 20.5 1.0
C29 C:3KR3800 3.0 20.9 1.0
O C:THR245 3.4 25.6 1.0
CD2 C:LEU218 3.5 15.0 1.0
OG1 C:THR247 3.6 34.1 1.0
CD1 C:LEU218 3.9 14.8 1.0
C27 C:3KR3800 4.1 21.1 1.0
CG C:LEU218 4.1 15.4 1.0
C30 C:3KR3800 4.3 21.6 1.0
CD1 C:LEU239 4.3 20.8 1.0
O C:HOH483 4.3 29.4 1.0
CB C:LEU218 4.5 13.9 1.0
CE1 C:PHE252 4.6 27.0 1.0
C C:THR245 4.6 25.6 1.0
OG1 C:THR245 4.6 25.3 1.0
N C:THR245 5.0 23.8 1.0

Fluorine binding site 8 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 8 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3800

b:23.9
occ:1.00
 F34 C:3KR3800 0.0 23.9 1.0
C32 C:3KR3800 1.4 22.0 1.0
F35 C:3KR3800 2.2 21.5 1.0
F33 C:3KR3800 2.2 21.6 1.0
O31 C:3KR3800 2.3 21.1 1.0
C28 C:3KR3800 2.9 20.5 1.0
O C:HOH483 3.0 29.4 1.0
C27 C:3KR3800 3.4 21.1 1.0
CA C:LEU239 3.4 20.7 1.0
O C:HOH274 3.5 20.6 1.0
CD1 C:LEU239 3.7 20.8 1.0
O C:ALA238 3.7 20.9 1.0
C29 C:3KR3800 3.8 20.9 1.0
N C:LEU239 4.0 21.2 1.0
O C:LEU239 4.1 20.4 1.0
C C:ALA238 4.2 21.5 1.0
CB C:LEU239 4.2 20.5 1.0
C C:LEU239 4.2 20.6 1.0
O C:HOH304 4.5 20.0 1.0
C26 C:3KR3800 4.5 20.6 1.0
CG C:LEU239 4.6 20.9 1.0
C30 C:3KR3800 4.9 21.6 1.0
O C:GLY237 4.9 24.6 1.0
CE1 C:PHE252 4.9 27.0 1.0
OG1 C:THR245 5.0 25.3 1.0

Fluorine binding site 9 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 9 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3800

b:21.5
occ:1.00
 F35 C:3KR3800 0.0 21.5 1.0
C32 C:3KR3800 1.3 22.0 1.0
F34 C:3KR3800 2.2 23.9 1.0
F33 C:3KR3800 2.2 21.6 1.0
O31 C:3KR3800 2.3 21.1 1.0
O C:HOH483 2.6 29.4 1.0
OG1 C:THR245 3.2 25.3 1.0
O C:HOH274 3.4 20.6 1.0
OG1 C:THR247 3.5 34.1 1.0
C28 C:3KR3800 3.6 20.5 1.0
O C:HOH304 3.8 20.0 1.0
O C:THR245 3.8 25.6 1.0
C29 C:3KR3800 4.4 20.9 1.0
C27 C:3KR3800 4.4 21.1 1.0
CB C:THR245 4.5 25.1 1.0
C C:THR245 4.5 25.6 1.0
CB C:THR247 4.7 32.8 1.0
CG2 C:THR247 4.8 33.4 1.0
N C:THR245 4.9 23.8 1.0
CA C:THR245 4.9 24.9 1.0

Fluorine binding site 10 out of 12 in 3kry

Go back to Fluorine Binding Sites List in 3kry
Fluorine binding site 10 out of 12 in the Crystal Structure of Mmp-13 in Complex with Sc-78080


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Mmp-13 in Complex with Sc-78080 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F4800

b:25.4
occ:1.00
 F33 D:3KR4800 0.0 25.4 1.0
C32 D:3KR4800 1.3 23.6 1.0
F35 D:3KR4800 2.2 24.2 1.0
F34 D:3KR4800 2.2 24.7 1.0
O31 D:3KR4800 2.2 22.6 1.0
C28 D:3KR4800 2.9 21.2 1.0
OG1 D:THR247 3.0 29.7 1.0
C29 D:3KR4800 3.1 21.9 1.0
O D:THR245 3.4 23.7 1.0
CD1 D:LEU218 3.6 15.3 1.0
CD2 D:LEU218 3.6 15.1 1.0
C27 D:3KR4800 4.1 21.6 1.0
CG D:LEU218 4.1 16.2 1.0
CB D:THR247 4.2 29.1 1.0
CD1 D:LEU239 4.2 18.9 1.0
C30 D:3KR4800 4.4 22.2 1.0
OG1 D:THR245 4.4 23.0 1.0
CG2 D:THR247 4.4 30.0 1.0
CB D:LEU218 4.5 15.0 1.0
CE1 D:PHE252 4.5 24.0 1.0
C D:THR245 4.5 23.8 1.0
N D:THR245 5.0 22.1 1.0

Reference:

D.P.Becker, T.E.Barta, L.J.Bedell, T.L.Boehm, B.R.Bond, J.Carroll, C.P.Carron, G.A.Decrescenzo, A.M.Easton, J.N.Freskos, C.L.Funckes-Shippy, M.Heron, S.Hockerman, C.P.Howard, J.R.Kiefer, M.H.Li, K.J.Mathis, J.J.Mcdonald, P.P.Mehta, G.E.Munie, T.Sunyer, C.A.Swearingen, C.I.Villamil, D.Welsch, J.M.Williams, Y.Yu, J.Yao. Orally-Active Mmp-1 Sparing Alpha-Tetrahydropyranyl and Alpha-Piperidinyl Sulfone Matrix Metalloproteinase (Mmp) Inhibitors with Efficacy in Cancer, Arthritis, and Cardiovascular Disease J.Med.Chem. V. 53 6653 2010.
ISSN: ISSN 0022-2623
PubMed: 20726512
DOI: 10.1021/JM100669J
Page generated: Mon Jul 14 17:32:19 2025

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