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Fluorine in PDB 3kek: Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound

Protein crystallography data

The structure of Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound, PDB code: 3kek was solved by H.-S.Shieh, B.Collins, M.E.Schnute, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.14 / 1.97
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.846, 95.740, 36.443, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.8

Other elements in 3kek:

The structure of Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Zinc (Zn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound (pdb code 3kek). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound, PDB code: 3kek:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3kek

Go back to Fluorine Binding Sites List in 3kek
Fluorine binding site 1 out of 2 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound


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 Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:17.5
occ:1.00
F32 A:3EK801 0.0 17.5 1.0
C27 A:3EK801 1.3 15.3 1.0
C26 A:3EK801 2.3 15.3 1.0
C28 A:3EK801 2.4 15.6 1.0
O A:HOH2039 3.0 13.7 1.0
CG1 A:VAL219 3.4 11.1 1.0
CG2 A:VAL219 3.5 13.9 1.0
CA A:VAL219 3.6 13.0 1.0
C25 A:3EK801 3.6 15.3 1.0
C29 A:3EK801 3.6 15.7 1.0
CB A:VAL219 3.7 12.9 1.0
CD2 A:HIS222 4.0 11.3 1.0
CG A:HIS222 4.0 12.1 1.0
CD1 A:LEU185 4.0 12.7 1.0
CB A:HIS222 4.1 12.3 1.0
C24 A:3EK801 4.1 16.1 1.0
O A:VAL219 4.2 12.4 1.0
CD1 A:TYR244 4.3 15.1 1.0
C A:VAL219 4.4 12.2 1.0
N A:VAL219 4.6 13.7 1.0
NE2 A:HIS222 4.6 13.2 1.0
ND1 A:HIS222 4.6 12.6 1.0
CB A:TYR244 4.6 16.7 1.0
OE2 A:GLU223 4.7 14.4 1.0
O A:LEU218 4.9 13.5 1.0
CB A:LEU185 4.9 13.9 1.0
CE1 A:HIS222 4.9 13.6 1.0
CG A:TYR244 5.0 15.7 1.0

Fluorine binding site 2 out of 2 in 3kek

Go back to Fluorine Binding Sites List in 3kek
Fluorine binding site 2 out of 2 in the Crystal Structure of Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound


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 Human Mmp-13 Complexed with A (Pyridin-4-Yl)-2H- Tetrazole Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.1
occ:1.00
F32 B:3EK801 0.0 21.1 1.0
C27 B:3EK801 1.3 21.3 1.0
C28 B:3EK801 2.3 21.0 1.0
C26 B:3EK801 2.4 22.4 1.0
O B:HOH2101 2.9 30.4 1.0
CG1 B:VAL219 3.5 15.1 1.0
C29 B:3EK801 3.6 21.7 1.0
C25 B:3EK801 3.6 21.4 1.0
CA B:VAL219 3.7 14.9 1.0
CG2 B:VAL219 3.7 15.8 1.0
CB B:VAL219 3.8 15.2 1.0
CG B:HIS222 3.8 16.7 1.0
CD2 B:HIS222 3.9 17.4 1.0
CB B:HIS222 3.9 16.0 1.0
C24 B:3EK801 4.1 21.7 1.0
CD1 B:TYR244 4.1 21.3 1.0
CD1 B:LEU185 4.2 26.7 1.0
O B:VAL219 4.3 14.1 1.0
ND1 B:HIS222 4.4 17.8 1.0
C B:VAL219 4.5 14.3 1.0
NE2 B:HIS222 4.5 19.7 1.0
OE2 B:GLU223 4.6 19.3 1.0
N B:VAL219 4.6 15.5 1.0
CE1 B:HIS222 4.8 19.2 1.0
O B:LEU218 4.8 15.8 1.0
CE1 B:TYR244 4.9 20.2 1.0
CB B:TYR244 5.0 24.2 1.0

Reference:

M.E.Schnute, P.M.O'brien, J.Nahra, M.Morris, W.Howard Roark, C.E.Hanau, P.G.Ruminski, J.A.Scholten, T.R.Fletcher, B.C.Hamper, J.N.Carroll, W.C.Patt, H.S.Shieh, B.Collins, A.G.Pavlovsky, K.E.Palmquist, K.W.Aston, J.Hitchcock, M.D.Rogers, J.Mcdonald, A.R.Johnson, G.E.Munie, A.J.Wittwer, C.F.Man, S.L.Settle, O.Nemirovskiy, L.E.Vickery, A.Agawal, R.D.Dyer, T.Sunyer. Discovery of (Pyridin-4-Yl)-2H-Tetrazole As A Novel Scaffold to Identify Highly Selective Matrix Metalloproteinase-13 Inhibitors For the Treatment of Osteoarthritis. Bioorg.Med.Chem.Lett. V. 20 576 2009.
ISSN: ISSN 0960-894X
PubMed: 20005097
DOI: 10.1016/J.BMCL.2009.11.081
Page generated: Sun Dec 13 11:49:15 2020

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