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Chlorine in PDB 3kdc: Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074

Enzymatic activity of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074

All present enzymatic activity of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074, PDB code: 3kdc was solved by E.E.Chufan, Y.Kawasaki, E.Freire, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.28 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.310, 86.095, 46.369, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 23.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 (pdb code 3kdc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074, PDB code: 3kdc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3kdc

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Chlorine binding site 1 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl100

b:20.8
occ:0.60
 CL1 A:JZP100 0.0 20.8 0.6
C37 A:JZP100 0.7 14.1 0.4
C38 A:JZP100 0.8 14.2 0.4
C36 A:JZP100 1.7 14.0 0.4
C42 A:JZP100 1.8 20.9 0.6
C34 A:JZP100 1.8 14.3 0.4
C32 A:JZP100 2.4 14.3 0.4
C33 A:JZP100 2.4 14.3 0.4
C41 A:JZP100 2.8 21.2 0.6
C45 A:JZP100 2.8 20.5 0.6
C39 A:JZP100 3.1 14.1 0.4
O2 A:JZP100 3.1 19.4 0.6
C21 A:JZP100 3.5 17.5 0.6
N B:ASP30 3.7 20.4 1.0
O B:ASP30 3.7 20.5 1.0
C31 A:JZP100 3.7 14.5 0.4
CG2 B:VAL32 3.7 21.7 1.0
CB B:ASP30 3.8 20.7 1.0
C35 A:JZP100 4.0 14.0 0.4
CD1 B:ILE47 4.0 23.9 1.0
CA B:ASP30 4.1 20.8 1.0
C B:ASP30 4.1 20.5 1.0
CB B:ALA28 4.1 19.3 1.0
C40 A:JZP100 4.1 20.9 0.6
C46 A:JZP100 4.2 20.8 0.6
N B:ASP29 4.3 20.2 1.0
CG2 B:ILE47 4.3 23.9 1.0
CB B:ILE47 4.4 24.0 1.0
OD2 B:ASP30 4.4 24.1 1.0
CA B:ALA28 4.5 19.6 1.0
CG B:ASP30 4.5 22.4 1.0
CD1 A:ILE50 4.5 21.9 0.5
O7 A:JZP100 4.6 14.1 0.4
N4 A:JZP100 4.6 14.8 0.4
C47 A:JZP100 4.7 21.2 0.6
C B:ALA28 4.7 19.8 1.0
C12 A:JZP100 4.7 16.4 0.6
CG1 B:ILE47 4.8 23.7 1.0
C B:ASP29 4.8 20.4 1.0
CD1 B:ILE84 4.8 20.6 0.7
CD1 B:LEU76 4.9 19.4 1.0
CD1 A:ILE50 4.9 21.2 0.5
CA B:ASP29 5.0 20.4 1.0

Chlorine binding site 2 out of 8 in 3kdc

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Chlorine binding site 2 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl100

b:23.1
occ:0.40
 CL1 A:JZP100 0.0 23.1 0.4
C37 A:JZP100 0.3 14.5 0.6
C36 A:JZP100 1.5 14.2 0.6
C38 A:JZP100 1.6 14.7 0.6
C42 A:JZP100 1.8 22.8 0.4
C39 A:JZP100 2.6 14.2 0.6
C34 A:JZP100 2.7 14.5 0.6
C32 A:JZP100 2.7 14.1 0.6
C41 A:JZP100 2.8 23.0 0.4
C45 A:JZP100 2.9 22.7 0.4
C33 A:JZP100 3.1 14.6 0.6
O2 A:JZP100 3.2 21.9 0.4
O A:ASP30 3.4 21.1 0.3
C21 A:JZP100 3.4 20.5 0.4
O A:ASP30 3.5 21.1 0.7
CB A:ASP30 3.7 21.6 0.7
CD1 A:ILE47 3.8 20.2 1.0
N A:ASP30 3.8 21.4 0.7
N A:ASP30 3.8 21.2 0.3
C35 A:JZP100 3.8 14.0 0.6
C A:ASP30 3.8 21.2 0.3
C A:ASP30 3.9 21.3 0.7
C31 A:JZP100 3.9 14.1 0.6
CB A:ASP30 3.9 21.2 0.3
CA A:ASP30 4.0 21.5 0.7
CA A:ASP30 4.0 21.2 0.3
C40 A:JZP100 4.1 22.8 0.4
CD1 A:LEU76 4.1 19.3 1.0
C46 A:JZP100 4.2 22.9 0.4
CG2 A:ILE47 4.3 20.3 1.0
OD2 A:ASP30 4.4 23.4 0.7
CB A:ILE47 4.4 20.6 1.0
CB A:ALA28 4.5 20.3 1.0
CG A:ASP30 4.5 22.5 0.7
CG1 A:VAL32 4.6 21.4 1.0
C47 A:JZP100 4.6 22.9 0.4
O7 A:JZP100 4.7 13.3 0.6
N A:ASP29 4.7 20.6 1.0
CG1 A:ILE47 4.7 20.6 1.0
CB A:VAL32 4.7 21.0 1.0
N A:THR31 4.7 21.3 1.0
CD1 A:ILE84 4.8 20.5 0.3
C12 A:JZP100 4.9 19.6 0.4
CA A:ALA28 4.9 20.3 1.0
N4 A:JZP100 4.9 13.9 0.6
C A:ASP29 5.0 21.2 1.0

Chlorine binding site 3 out of 8 in 3kdc

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Chlorine binding site 3 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl100

b:22.3
occ:0.60
 CL2 A:JZP100 0.0 22.3 0.6
C35 A:JZP100 1.8 14.0 0.4
C46 A:JZP100 1.8 20.8 0.6
O7 A:JZP100 1.9 14.1 0.4
C31 A:JZP100 2.4 14.5 0.4
N4 A:JZP100 2.5 14.8 0.4
C47 A:JZP100 2.8 21.2 0.6
C45 A:JZP100 2.8 20.5 0.6
C29 A:JZP100 2.9 15.5 0.4
O B:HOH194 3.0 31.0 1.0
O2 A:JZP100 3.1 19.4 0.6
C26 A:JZP100 3.1 15.7 0.6
O B:HOH169 3.2 23.2 1.0
C39 A:JZP100 3.2 14.1 0.4
C20 A:JZP100 3.4 15.4 0.4
O B:GLY48 3.5 23.1 1.0
C27 A:JZP100 3.5 15.9 0.6
C32 A:JZP100 3.7 14.3 0.4
O B:HOH119 3.7 12.8 1.0
C25 A:JZP100 3.7 16.1 0.6
C21 A:JZP100 3.8 17.5 0.6
O A:HOH137 3.9 22.6 1.0
C18 A:JZP100 3.9 15.7 0.4
C17 A:JZP100 4.1 15.7 0.4
C36 A:JZP100 4.1 14.0 0.4
C40 A:JZP100 4.1 20.9 0.6
O4 A:JZP100 4.1 15.5 0.4
C42 A:JZP100 4.2 20.9 0.6
O B:GLY27 4.2 18.9 1.0
N2 A:JZP100 4.3 15.4 0.6
C22 A:JZP100 4.4 15.9 0.6
NH2 A:ARG8 4.5 27.7 1.0
C12 A:JZP100 4.5 16.4 0.6
O B:HOH113 4.6 18.3 1.0
OD1 B:ASP29 4.6 21.0 1.0
C24 A:JZP100 4.6 16.2 0.6
C30 A:JZP100 4.6 15.6 0.4
C41 A:JZP100 4.6 21.2 0.6
C B:GLY48 4.7 22.9 1.0
CG B:ASP29 4.7 21.3 1.0
OD2 B:ASP29 4.8 23.6 1.0
C23 A:JZP100 4.9 16.2 0.6
C33 A:JZP100 4.9 14.3 0.4
CZ A:ARG8 5.0 28.0 1.0

Chlorine binding site 4 out of 8 in 3kdc

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Chlorine binding site 4 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl100

b:23.3
occ:0.40
 CL2 A:JZP100 0.0 23.3 0.4
O7 A:JZP100 1.4 13.3 0.6
C46 A:JZP100 1.8 22.9 0.4
C35 A:JZP100 2.0 14.0 0.6
N4 A:JZP100 2.4 13.9 0.6
C31 A:JZP100 2.6 14.1 0.6
C47 A:JZP100 2.8 22.9 0.4
C45 A:JZP100 2.8 22.7 0.4
C29 A:JZP100 3.0 12.8 0.6
O A:HOH197 3.1 38.9 1.0
O2 A:JZP100 3.1 21.9 0.4
C27 A:JZP100 3.3 17.2 0.4
C20 A:JZP100 3.3 14.1 0.6
C26 A:JZP100 3.3 17.2 0.4
C39 A:JZP100 3.4 14.2 0.6
O A:HOH118 3.6 11.9 1.0
O A:GLY48 3.7 22.1 1.0
C32 A:JZP100 3.8 14.1 0.6
O A:HOH188 3.9 47.5 1.0
C17 A:JZP100 3.9 13.7 0.6
C18 A:JZP100 3.9 13.5 0.6
O A:GLY27 3.9 19.9 1.0
C21 A:JZP100 3.9 20.5 0.4
N2 A:JZP100 4.0 18.7 0.4
C40 A:JZP100 4.1 22.8 0.4
O B:HOH108 4.1 29.9 1.0
O4 A:JZP100 4.2 14.2 0.6
C42 A:JZP100 4.2 22.8 0.4
C12 A:JZP100 4.2 19.6 0.4
C36 A:JZP100 4.2 14.2 0.6
C22 A:JZP100 4.3 17.6 0.4
C25 A:JZP100 4.4 17.6 0.4
C30 A:JZP100 4.4 13.2 0.6
OD2 A:ASP29 4.4 23.0 1.0
CG A:ASP29 4.5 20.9 1.0
OD1 A:ASP29 4.5 21.6 1.0
N A:ASP29 4.6 20.6 1.0
C41 A:JZP100 4.6 23.0 0.4
C A:GLY48 4.9 21.9 1.0
O A:HOH111 4.9 14.4 1.0
C15 A:JZP100 4.9 17.4 0.4
CA A:ALA28 4.9 20.3 1.0
C33 A:JZP100 5.0 14.6 0.6

Chlorine binding site 5 out of 8 in 3kdc

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Chlorine binding site 5 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:23.7
occ:1.00
 O A:HOH227 3.2 37.5 1.0
N A:THR74 3.2 22.8 1.0
ND2 A:ASN88 3.3 20.6 1.0
CA A:GLY73 3.8 23.1 1.0
CB A:THR74 3.8 22.7 1.0
CB A:ASN88 3.8 19.2 1.0
OG1 A:THR74 3.8 23.2 1.0
C A:GLY73 4.0 22.9 1.0
CG A:ASN88 4.0 19.6 1.0
CA A:THR74 4.1 22.6 1.0
O A:HOH193 4.2 31.8 1.0
O A:THR74 4.7 22.3 1.0
O A:HOH148 4.7 42.0 1.0
O A:ASN88 4.7 18.9 1.0
CA A:ASN88 4.9 19.0 1.0
OD1 A:ASP30 4.9 20.7 0.3
C A:THR74 4.9 22.3 1.0

Chlorine binding site 6 out of 8 in 3kdc

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Chlorine binding site 6 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:28.0
occ:0.50
 O A:ILE50 2.0 21.7 0.5
N A:GLY51 3.0 21.0 0.5
C A:ILE50 3.1 21.5 0.5
O B:PRO79 3.2 21.8 1.0
CG2 B:ILE54 3.6 19.6 1.0
CA A:GLY51 3.6 20.7 0.5
C A:GLY51 3.8 20.5 0.5
N A:GLY52 3.9 20.5 1.0
C A:ILE50 3.9 21.1 0.5
N A:GLY51 4.0 21.2 0.5
CA A:ILE50 4.0 21.8 0.5
O A:GLY49 4.0 22.3 1.0
CA A:ILE50 4.0 21.4 0.5
CA A:GLY51 4.1 20.9 0.5
C A:GLY51 4.2 20.6 0.5
C B:PRO79 4.3 21.7 1.0
CD B:PRO81 4.4 22.2 1.0
CG B:PRO81 4.5 22.7 1.0
O A:GLY51 4.5 20.5 0.5
CD1 B:ILE54 4.7 19.0 1.0
CA A:GLY52 4.7 20.2 1.0
CB B:ILE54 4.9 19.6 1.0
C A:GLY49 4.9 22.0 1.0
CB B:PRO79 4.9 21.5 1.0
N A:ILE50 5.0 22.0 0.5
N A:ILE50 5.0 21.8 0.5
CB A:ILE50 5.0 21.5 0.5
CG2 A:ILE50 5.0 21.7 0.5

Chlorine binding site 7 out of 8 in 3kdc

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Chlorine binding site 7 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl100

b:23.8
occ:1.00
 O B:HOH180 2.9 22.1 1.0
N B:THR74 3.2 20.8 1.0
ND2 B:ASN88 3.2 19.1 1.0
CA B:GLY73 3.7 20.7 1.0
OG1 B:THR74 3.9 21.0 1.0
CB B:THR74 3.9 20.9 1.0
CB B:ASN88 3.9 19.7 1.0
C B:GLY73 3.9 20.6 1.0
CG B:ASN88 4.0 19.1 1.0
CA B:THR74 4.1 20.8 1.0
NE2 B:GLN92 4.4 20.0 1.0
O B:HOH176 4.4 15.4 1.0
O B:ASN88 4.5 20.3 1.0
CD2 B:LEU89 4.7 18.8 1.0
O B:HOH199 4.7 26.6 1.0
O B:THR74 4.7 21.1 1.0
O B:HOH141 4.8 35.3 1.0
C B:ASN88 4.8 19.9 1.0
CA B:ASN88 4.9 19.9 1.0
C B:THR74 5.0 21.0 1.0
N B:GLY73 5.0 20.8 1.0

Chlorine binding site 8 out of 8 in 3kdc

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Chlorine binding site 8 out of 8 in the Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Hiv-1 Protease (Q7K, L33I, L63I) in Complex with Kni-10074 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl101

b:24.1
occ:1.00
 NE1 B:TRP6 3.3 18.7 1.0
O A:HOH109 3.4 20.1 1.0
CZ2 B:TRP6 4.0 18.6 1.0
CE2 B:TRP6 4.0 18.9 1.0
CG2 B:THR4 4.1 20.7 1.0
CD1 B:TRP6 4.4 18.6 1.0
O A:HOH142 4.7 32.4 1.0
CB B:THR4 4.8 20.9 1.0
O A:HOH106 5.0 14.1 1.0

Reference:

Y.Kawasaki, E.E.Chufan, V.Lafont, K.Hidaka, Y.Kiso, L.Mario Amzel, E.Freire. How Much Binding Affinity Can Be Gained By Filling A Cavity? Chem.Biol.Drug Des. V. 75 143 2010.
ISSN: ISSN 1747-0277
PubMed: 20028396
DOI: 10.1111/J.1747-0285.2009.00921.X
Page generated: Sat Dec 12 09:50:52 2020

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