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Fluorine in PDB 4pyy: Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor

Enzymatic activity of Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor

All present enzymatic activity of Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor, PDB code: 4pyy was solved by A.Smirnov, E.Manakova, S.Grazulis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.76 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.240, 41.519, 71.936, 90.00, 104.42, 90.00
R / Rfree (%) 14.9 / 20

Other elements in 4pyy:

The structure of Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor (pdb code 4pyy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor, PDB code: 4pyy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4pyy

Go back to Fluorine Binding Sites List in 4pyy
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor


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 Carbonic Anhydrase Isozyme II with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:8.0
occ:0.50
 F20 A:V14302 0.0 8.0 0.5
C5 A:V14302 1.3 7.1 0.5
C3 A:V14302 2.0 15.3 0.5
C2 A:V14302 2.0 18.2 0.5
C1 A:V14302 2.0 20.3 0.5
C4 A:V14302 2.1 14.7 0.5
C6 A:V14302 2.2 18.1 0.5
C5 A:V14302 2.3 16.6 0.5
C6 A:V14302 2.3 7.5 0.5
C4 A:V14302 2.3 6.5 0.5
N19 A:V14302 2.7 7.2 0.5
O9 A:V14302 2.9 5.5 0.5
C14 A:V14302 2.9 7.4 0.5
F13 A:V14302 3.0 17.6 0.5
F12 A:V14302 3.0 17.6 0.5
CE1 A:HIS94 3.0 6.3 1.0
S7 A:V14302 3.1 5.7 0.5
C28 A:V14302 3.3 7.8 0.5
CG2 A:VAL121 3.3 7.3 1.0
N19 A:V14302 3.3 16.4 0.5
F20 A:V14302 3.4 18.5 0.5
S11 A:V14302 3.5 26.4 0.5
S7 A:V14302 3.5 11.2 0.5
C3 A:V14302 3.6 6.8 0.5
C1 A:V14302 3.6 7.7 0.5
O9 A:V14302 3.7 12.6 0.5
ND1 A:HIS94 3.8 6.0 1.0
NE2 A:HIS94 4.0 6.5 1.0
C28 A:V14302 4.0 13.1 0.5
NE2 A:GLN92 4.1 11.6 1.0
C2 A:V14302 4.1 7.5 0.5
O16 A:V14302 4.1 26.2 0.5
CD A:GLN92 4.2 11.1 1.0
CG1 A:VAL121 4.2 7.6 1.0
C14 A:V14302 4.2 15.0 0.5
OE1 A:GLN92 4.2 10.1 1.0
O8 A:V14302 4.2 5.3 0.5
N10 A:V14302 4.2 5.5 0.5
C15 A:V14302 4.3 25.7 0.5
CB A:VAL121 4.3 7.7 1.0
C18 A:V14302 4.3 24.6 0.5
C22 A:V14302 4.3 7.5 0.5
C27 A:V14302 4.5 8.3 0.5
N10 A:V14302 4.6 10.7 0.5
O17 A:V14302 4.7 27.6 0.5
O8 A:V14302 4.7 11.9 0.5
F12 A:V14302 4.7 6.9 0.5
O A:HOH572 4.8 32.0 1.0
ZN A:ZN301 4.9 7.3 1.0
CG A:HIS94 4.9 6.3 1.0
CD2 A:HIS94 5.0 6.5 1.0
O21 A:V14302 5.0 10.8 0.5

Fluorine binding site 2 out of 6 in 4pyy

Go back to Fluorine Binding Sites List in 4pyy
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor


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 Carbonic Anhydrase Isozyme II with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:18.5
occ:0.50
 F20 A:V14302 0.0 18.5 0.5
C5 A:V14302 1.4 16.6 0.5
C4 A:V14302 1.9 6.5 0.5
N10 A:V14302 2.0 5.5 0.5
C3 A:V14302 2.3 6.8 0.5
S7 A:V14302 2.3 5.7 0.5
C4 A:V14302 2.4 14.7 0.5
C6 A:V14302 2.5 18.1 0.5
F12 A:V14302 2.6 6.9 0.5
C14 A:V14302 2.7 15.0 0.5
C5 A:V14302 2.8 7.1 0.5
N10 A:V14302 2.8 10.7 0.5
N19 A:V14302 2.9 16.4 0.5
S7 A:V14302 3.0 11.2 0.5
C2 A:V14302 3.2 7.5 0.5
C28 A:V14302 3.3 13.1 0.5
C26 A:V14302 3.3 11.9 0.5
ZN A:ZN301 3.3 7.3 1.0
O8 A:V14302 3.4 5.3 0.5
F20 A:V14302 3.4 8.0 0.5
NE2 A:HIS94 3.4 6.5 1.0
O9 A:V14302 3.5 5.5 0.5
C6 A:V14302 3.6 7.5 0.5
CG2 A:THR200 3.7 11.5 1.0
C1 A:V14302 3.7 20.3 0.5
C3 A:V14302 3.7 15.3 0.5
CE1 A:HIS94 3.8 6.3 1.0
C1 A:V14302 3.8 7.7 0.5
C25 A:V14302 3.9 11.6 0.5
C22 A:V14302 4.0 14.6 0.5
OG1 A:THR200 4.0 15.0 1.0
O8 A:V14302 4.1 11.9 0.5
C27 A:V14302 4.1 12.7 0.5
O9 A:V14302 4.1 12.6 0.5
F13 A:V14302 4.2 7.8 0.5
OG1 A:THR199 4.2 5.8 1.0
C2 A:V14302 4.3 18.2 0.5
NE2 A:HIS96 4.3 6.5 1.0
CE1 A:HIS96 4.3 6.1 1.0
CD2 A:HIS94 4.3 6.5 1.0
CB A:THR200 4.5 10.9 1.0
O21 A:V14302 4.6 10.8 0.5
N A:THR200 4.6 7.9 1.0
C23 A:V14302 4.6 12.6 0.5
C24 A:V14302 4.7 13.2 0.5
ND1 A:HIS94 4.7 6.0 1.0
N19 A:V14302 4.8 7.2 0.5
F12 A:V14302 4.8 17.6 0.5

Fluorine binding site 3 out of 6 in 4pyy

Go back to Fluorine Binding Sites List in 4pyy
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor


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 Human Carbonic Anhydrase Isozyme II with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:6.9
occ:0.50
 F12 A:V14302 0.0 6.9 0.5
C3 A:V14302 1.3 6.8 0.5
C2 A:V14302 2.3 7.5 0.5
C4 A:V14302 2.4 6.5 0.5
F20 A:V14302 2.6 18.5 0.5
C5 A:V14302 2.6 16.6 0.5
F13 A:V14302 2.7 7.8 0.5
O8 A:V14302 2.7 5.3 0.5
N A:THR200 2.8 7.9 1.0
S7 A:V14302 2.9 5.7 0.5
C4 A:V14302 2.9 14.7 0.5
N A:THR199 3.1 5.8 1.0
OG1 A:THR200 3.1 15.0 1.0
N10 A:V14302 3.2 5.5 0.5
S7 A:V14302 3.3 11.2 0.5
O8 A:V14302 3.3 11.9 0.5
C6 A:V14302 3.4 18.1 0.5
CB A:LEU198 3.4 7.9 1.0
N10 A:V14302 3.5 10.7 0.5
CG2 A:THR200 3.5 11.5 1.0
CA A:THR200 3.6 9.0 1.0
O A:THR200 3.6 8.7 1.0
CB A:THR200 3.6 10.9 1.0
C5 A:V14302 3.6 7.1 0.5
C1 A:V14302 3.6 7.7 0.5
C A:LEU198 3.7 7.0 1.0
C A:THR199 3.7 6.9 1.0
CA A:LEU198 3.7 7.0 1.0
C3 A:V14302 3.9 15.3 0.5
CA A:THR199 3.9 6.2 1.0
OG1 A:THR199 3.9 5.8 1.0
N19 A:V14302 4.0 16.4 0.5
C A:THR200 4.0 8.9 1.0
C6 A:V14302 4.1 7.5 0.5
CD2 A:LEU198 4.2 9.2 1.0
C1 A:V14302 4.2 20.3 0.5
C14 A:V14302 4.3 15.0 0.5
CG A:LEU198 4.3 8.3 1.0
C2 A:V14302 4.4 18.2 0.5
O9 A:V14302 4.4 5.5 0.5
CB A:THR199 4.5 5.8 1.0
O A:LEU198 4.6 7.2 1.0
CD1 A:LEU198 4.6 9.7 1.0
F12 A:V14302 4.7 17.6 0.5
F20 A:V14302 4.7 8.0 0.5
O A:THR199 4.8 7.6 1.0
O9 A:V14302 4.8 12.6 0.5
C22 A:V14302 4.9 14.6 0.5

Fluorine binding site 4 out of 6 in 4pyy

Go back to Fluorine Binding Sites List in 4pyy
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor


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 Human Carbonic Anhydrase Isozyme II with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:17.6
occ:0.50
 F12 A:V14302 0.0 17.6 0.5
C3 A:V14302 1.4 15.3 0.5
C2 A:V14302 2.3 18.2 0.5
C4 A:V14302 2.4 14.7 0.5
O9 A:V14302 2.7 5.5 0.5
F13 A:V14302 2.7 17.6 0.5
S7 A:V14302 2.9 11.2 0.5
O9 A:V14302 2.9 12.6 0.5
CD2 A:LEU198 3.0 9.2 1.0
F20 A:V14302 3.0 8.0 0.5
O8 A:V14302 3.0 5.3 0.5
S7 A:V14302 3.1 5.7 0.5
C4 A:V14302 3.1 6.5 0.5
C5 A:V14302 3.1 7.1 0.5
O8 A:V14302 3.1 11.9 0.5
CG2 A:VAL143 3.5 6.8 1.0
C1 A:V14302 3.6 20.3 0.5
C28 A:V14302 3.6 7.8 0.5
C5 A:V14302 3.7 16.6 0.5
CG1 A:VAL121 3.8 7.6 1.0
CG2 A:VAL121 3.9 7.3 1.0
CD1 A:LEU141 3.9 9.3 1.0
C3 A:V14302 4.0 6.8 0.5
C6 A:V14302 4.1 7.5 0.5
C6 A:V14302 4.1 18.1 0.5
C14 A:V14302 4.4 7.4 0.5
CB A:VAL121 4.5 7.7 1.0
CG A:LEU198 4.5 8.3 1.0
C27 A:V14302 4.6 8.3 0.5
N10 A:V14302 4.6 10.7 0.5
CG2 A:VAL207 4.7 6.8 1.0
F12 A:V14302 4.7 6.9 0.5
N19 A:V14302 4.7 7.2 0.5
N10 A:V14302 4.7 5.5 0.5
C2 A:V14302 4.8 7.5 0.5
CB A:VAL143 4.8 6.3 1.0
C1 A:V14302 4.8 7.7 0.5
CA A:LEU198 4.8 7.0 1.0
F20 A:V14302 4.8 18.5 0.5
CG1 A:VAL143 4.9 6.4 1.0
CB A:LEU198 4.9 7.9 1.0
S11 A:V14302 5.0 26.4 0.5

Fluorine binding site 5 out of 6 in 4pyy

Go back to Fluorine Binding Sites List in 4pyy
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor


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 Human Carbonic Anhydrase Isozyme II with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:7.8
occ:0.50
 F13 A:V14302 0.0 7.8 0.5
C2 A:V14302 1.4 7.5 0.5
C3 A:V14302 2.4 6.8 0.5
C1 A:V14302 2.4 7.7 0.5
OG1 A:THR200 2.6 15.0 1.0
F12 A:V14302 2.7 6.9 0.5
S11 A:V14302 2.9 9.0 0.5
O16 A:V14302 3.0 8.9 0.5
O A:THR200 3.1 8.7 1.0
O A:PRO201 3.1 12.9 1.0
C15 A:V14302 3.1 9.5 0.5
C6 A:V14302 3.5 18.1 0.5
N19 A:V14302 3.5 16.4 0.5
C A:THR200 3.6 8.9 1.0
C4 A:V14302 3.6 6.5 0.5
C6 A:V14302 3.7 7.5 0.5
C A:PRO201 3.7 10.4 1.0
CD1 A:LEU198 3.7 9.7 1.0
CD A:PRO202 3.8 12.1 1.0
C5 A:V14302 3.8 16.6 0.5
CB A:THR200 3.8 10.9 1.0
O17 A:V14302 3.8 27.6 0.5
C1 A:V14302 3.9 20.3 0.5
CB A:LEU198 3.9 7.9 1.0
C22 A:V14302 4.0 14.6 0.5
N A:PRO202 4.0 10.1 1.0
C18 A:V14302 4.0 10.1 0.5
CA A:THR200 4.1 9.0 1.0
C14 A:V14302 4.1 15.0 0.5
C5 A:V14302 4.1 7.1 0.5
N A:THR200 4.1 7.9 1.0
O21 A:V14302 4.2 10.8 0.5
F20 A:V14302 4.2 18.5 0.5
O17 A:V14302 4.3 9.0 0.5
CG A:LEU198 4.4 8.3 1.0
C4 A:V14302 4.5 14.7 0.5
N A:PRO201 4.5 9.1 1.0
CD2 A:LEU198 4.5 9.2 1.0
CG2 A:THR200 4.5 11.5 1.0
S11 A:V14302 4.6 26.4 0.5
C2 A:V14302 4.6 18.2 0.5
C23 A:V14302 4.7 12.6 0.5
CA A:PRO201 4.7 9.3 1.0
C3 A:V14302 4.8 15.3 0.5
O16 A:V14302 4.9 26.2 0.5
N19 A:V14302 4.9 7.2 0.5
N A:LEU203 5.0 8.7 1.0

Fluorine binding site 6 out of 6 in 4pyy

Go back to Fluorine Binding Sites List in 4pyy
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Carbonic Anhydrase Isozyme II with Inhibitor


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 Human Carbonic Anhydrase Isozyme II with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:17.6
occ:0.50
 F13 A:V14302 0.0 17.6 0.5
C28 A:V14302 0.9 7.8 0.5
C2 A:V14302 1.4 18.2 0.5
C27 A:V14302 2.0 8.3 0.5
C14 A:V14302 2.1 7.4 0.5
C1 A:V14302 2.4 20.3 0.5
C3 A:V14302 2.4 15.3 0.5
F12 A:V14302 2.7 17.6 0.5
S11 A:V14302 2.8 26.4 0.5
C6 A:V14302 2.9 7.5 0.5
N19 A:V14302 2.9 7.2 0.5
C15 A:V14302 2.9 25.7 0.5
C5 A:V14302 2.9 7.1 0.5
F20 A:V14302 3.0 8.0 0.5
C26 A:V14302 3.2 8.9 0.5
C22 A:V14302 3.4 7.5 0.5
CG1 A:VAL121 3.4 7.6 1.0
O17 A:V14302 3.5 27.6 0.5
C25 A:V14302 3.5 8.6 0.5
CD1 A:LEU141 3.5 9.3 1.0
CD2 A:LEU198 3.5 9.2 1.0
C4 A:V14302 3.7 14.7 0.5
C18 A:V14302 3.7 24.6 0.5
C1 A:V14302 3.7 7.7 0.5
C6 A:V14302 3.7 18.1 0.5
C4 A:V14302 3.8 6.5 0.5
C23 A:V14302 3.8 8.5 0.5
C5 A:V14302 4.3 16.6 0.5
C24 A:V14302 4.3 8.3 0.5
O16 A:V14302 4.3 26.2 0.5
C2 A:V14302 4.4 7.5 0.5
C3 A:V14302 4.4 6.8 0.5
CG2 A:VAL121 4.5 7.3 1.0
CB A:VAL121 4.6 7.7 1.0
O17 A:V14302 4.7 9.0 0.5
S11 A:V14302 4.7 9.0 0.5
N19 A:V14302 4.8 16.4 0.5
O16 A:V14302 4.8 8.9 0.5
O9 A:V14302 4.8 5.5 0.5
CG A:LEU198 4.9 8.3 1.0
S7 A:V14302 4.9 5.7 0.5
CD1 A:LEU198 4.9 9.7 1.0
CG A:LEU141 5.0 9.0 1.0
O21 A:V14302 5.0 24.7 0.5

Reference:

V.Dudutiene, J.Matuliene, A.Smirnov, D.D.Timm, A.Zubriene, L.Baranauskiene, V.Morkunaite, J.Smirnoviene, V.Michailoviene, V.Juozapaitiene, A.Mickeviciute, J.Kazokaite, S.Baksyte, A.Kasiliauskaite, J.Jachno, J.Revuckiene, M.Kisonaite, V.Pilipuityte, E.Ivanauskaite, G.Milinaviciute, V.Smirnovas, V.Petrikaite, V.Kairys, V.Petrauskas, P.Norvaisas, D.Linge, P.Gibieza, E.Capkauskaite, A.Zaksauskas, E.Kazlauskas, E.Manakova, S.Grazulis, J.E.Ladbury, D.Matulis. Discovery and Characterization of Novel Selective Inhibitors of Carbonic Anhydrase IX. J.Med.Chem. V. 57 9435 2014.
ISSN: ISSN 0022-2623
PubMed: 25358084
DOI: 10.1021/JM501003K
Page generated: Tue Jul 15 00:13:45 2025

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