Fluorine in PDB 6d0e: X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13

Protein crystallography data

The structure of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13, PDB code: 6d0e was solved by R.S.Yedidi, H.Hayashi, A.K.Ghosh, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.34 / 1.95
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 62.686, 62.686, 82.181, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13 (pdb code 6d0e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13, PDB code: 6d0e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6d0e

Go back to Fluorine Binding Sites List in 6d0e
Fluorine binding site 1 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:24.1
occ:0.52
F01 B:FQ1500 0.0 24.1 0.5
C33 B:FQ1500 1.3 20.0 0.5
C09 B:FQ1500 2.3 19.6 0.5
C06 B:FQ1500 2.3 19.5 0.5
CG A:PRO81 2.9 28.4 1.0
CD A:PRO81 3.1 28.6 1.0
C B:GLY49 3.1 24.6 1.0
N B:ILE50 3.2 20.0 1.0
C13 B:FQ1500 3.3 20.1 0.5
CA B:ILE50 3.4 23.6 1.0
O B:GLY49 3.5 21.5 1.0
CA B:GLY49 3.6 21.5 1.0
C15 B:FQ1500 3.6 18.4 0.5
C34 B:FQ1500 3.6 20.9 0.5
C07 B:FQ1500 3.6 20.1 0.5
C14 B:FQ1500 3.9 21.1 0.5
CB B:ILE50 4.1 24.1 1.0
C08 B:FQ1500 4.1 19.3 0.5
CG1 B:ILE50 4.3 28.2 1.0
CB A:PRO81 4.3 28.0 1.0
N A:PRO81 4.4 28.1 1.0
OG1 A:THR80 4.5 21.9 1.0
C12 B:FQ1500 4.5 18.9 0.5
N B:GLY49 4.5 19.9 1.0
C B:ILE50 4.6 29.0 1.0
F02 B:FQ1500 4.7 19.1 0.5
CG2 A:VAL82 4.8 23.8 0.3
O B:HOH601 4.8 17.3 1.0
C32 B:FQ1500 4.8 15.3 0.5
N A:VAL82 4.8 27.3 1.0
O22 B:FQ1500 4.9 17.0 0.5
O B:HOH621 4.9 36.0 1.0
O B:GLY48 4.9 19.9 0.9
O10 B:FQ1500 4.9 18.3 0.5
CA A:PRO81 4.9 33.0 1.0
CG2 A:VAL82 5.0 29.0 0.7

Fluorine binding site 2 out of 4 in 6d0e

Go back to Fluorine Binding Sites List in 6d0e
Fluorine binding site 2 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:23.7
occ:0.48
F01 B:FQ1500 0.0 23.7 0.5
C33 B:FQ1500 1.3 22.6 0.5
C06 B:FQ1500 2.3 19.5 0.5
C09 B:FQ1500 2.4 18.6 0.5
CG B:PRO81 2.8 31.5 1.0
N A:ILE50 3.0 21.7 1.0
C A:GLY49 3.0 25.8 1.0
CD B:PRO81 3.1 25.9 1.0
C13 B:FQ1500 3.3 20.8 0.5
CA A:ILE50 3.4 22.7 1.0
C15 B:FQ1500 3.4 19.8 0.5
CA A:GLY49 3.4 24.0 1.0
O A:GLY49 3.6 20.7 1.0
C07 B:FQ1500 3.6 20.2 0.5
C34 B:FQ1500 3.6 20.0 0.5
CG1 A:ILE50 3.8 27.5 1.0
CB A:ILE50 4.1 24.5 1.0
C14 B:FQ1500 4.1 21.3 0.5
C08 B:FQ1500 4.1 20.2 0.5
CB B:PRO81 4.3 28.6 1.0
N B:PRO81 4.4 29.1 1.0
OG1 B:THR80 4.5 20.8 1.0
C12 B:FQ1500 4.5 19.1 0.5
O B:HOH601 4.5 17.3 1.0
N A:GLY49 4.5 20.1 1.0
C A:ILE50 4.6 28.8 1.0
F02 B:FQ1500 4.7 19.2 0.5
O10 B:FQ1500 4.8 19.3 0.5
C32 B:FQ1500 4.8 16.7 0.5
O9 B:FQ1500 4.9 19.5 0.5
O22 B:FQ1500 4.9 18.5 0.5
N B:VAL82 4.9 30.6 1.0
CA B:PRO81 4.9 31.6 1.0

Fluorine binding site 3 out of 4 in 6d0e

Go back to Fluorine Binding Sites List in 6d0e
Fluorine binding site 3 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:19.1
occ:0.52
F02 B:FQ1500 0.0 19.1 0.5
C34 B:FQ1500 1.3 20.9 0.5
C09 B:FQ1500 2.3 19.6 0.5
C08 B:FQ1500 2.4 19.3 0.5
CG2 A:VAL82 3.1 29.0 0.7
C29 B:FQ1500 3.1 16.1 0.5
C14 B:FQ1500 3.2 21.1 0.5
CG1 A:VAL82 3.3 28.9 0.3
C30 B:FQ1500 3.3 18.0 0.5
NH2 A:ARG8 3.4 27.6 1.0
C33 B:FQ1500 3.6 20.0 0.5
C07 B:FQ1500 3.6 20.1 0.5
CG2 A:VAL82 3.7 23.8 0.3
O B:HOH615 3.7 22.9 1.0
CZ A:ARG8 3.8 36.1 1.0
C13 B:FQ1500 3.8 20.1 0.5
CB A:VAL82 3.9 27.0 0.7
NH1 A:ARG8 3.9 32.3 1.0
CB A:VAL82 4.0 27.0 0.3
C12 B:FQ1500 4.1 18.9 0.5
C06 B:FQ1500 4.1 19.5 0.5
CG1 A:VAL82 4.4 21.4 0.7
O28 B:FQ1500 4.5 15.7 0.5
O B:GLY27 4.6 19.4 1.0
NE A:ARG8 4.6 32.3 1.0
CD2 A:LEU23 4.7 18.6 1.0
F01 B:FQ1500 4.7 24.1 0.5
C31 B:FQ1500 4.9 17.3 0.5
C32 B:FQ1500 4.9 15.3 0.5

Fluorine binding site 4 out of 4 in 6d0e

Go back to Fluorine Binding Sites List in 6d0e
Fluorine binding site 4 out of 4 in the X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Crystal Structure of Wild Type Hiv-1 Protease in Complex with Grl-084-13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:19.2
occ:0.48
F02 B:FQ1500 0.0 19.2 0.5
C34 B:FQ1500 1.3 20.0 0.5
C08 B:FQ1500 2.3 20.2 0.5
C09 B:FQ1500 2.3 18.6 0.5
C14 B:FQ1500 3.1 21.3 0.5
C29 B:FQ1500 3.2 15.7 0.5
CG1 B:VAL82 3.4 35.2 1.0
C30 B:FQ1500 3.4 18.1 0.5
NH2 B:ARG8 3.5 30.8 1.0
CG2 B:VAL82 3.6 28.3 1.0
C33 B:FQ1500 3.6 22.6 0.5
C07 B:FQ1500 3.6 20.2 0.5
C13 B:FQ1500 3.7 20.8 0.5
O B:HOH623 3.7 25.7 1.0
CZ B:ARG8 3.9 37.8 1.0
NH1 B:ARG8 4.1 33.7 1.0
C12 B:FQ1500 4.1 19.1 0.5
C06 B:FQ1500 4.1 19.5 0.5
CB B:VAL82 4.1 35.4 1.0
CD1 B:LEU23 4.5 23.9 1.0
O28 B:FQ1500 4.6 16.2 0.5
NE B:ARG8 4.6 30.4 1.0
O A:GLY27 4.7 18.2 1.0
F01 B:FQ1500 4.7 23.7 0.5
C32 B:FQ1500 4.9 16.7 0.5
C31 B:FQ1500 4.9 17.6 0.5

Reference:

M.Amano, P.M.Salcedo-Gomez, R.S.Yedidi, R.Zhao, H.Hayashi, K.Hasegawa, T.Nakamura, C.D.Martyr, A.K.Ghosh, H.Mitsuya. Novel Central Nervous System (Cns)-Targeting Protease Inhibitors For Drug-Resistant Hiv Infection and Hiv-Associated Cns Complications. Antimicrob.Agents Chemother. V. 63 2019.
ISSN: ESSN 1098-6596
PubMed: 31061155
DOI: 10.1128/AAC.00466-19
Page generated: Sun Dec 13 12:47:18 2020

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