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Chlorine in PDB 2v0m: Crystal Structure of Human P450 3A4 in Complex with Ketoconazole

Enzymatic activity of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole

All present enzymatic activity of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole:
1.14.13.67; 1.14.14.1;

Protein crystallography data

The structure of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole, PDB code: 2v0m was solved by T.Sjogren, M.Ekroos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.942, 66.363, 146.419, 90.00, 102.80, 90.00
R / Rfree (%) 21.8 / 27.1

Other elements in 2v0m:

The structure of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole (pdb code 2v0m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole, PDB code: 2v0m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 2v0m

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Chlorine binding site 1 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1500

b:37.9
occ:1.00
 CL1 A:KLN1500 0.0 37.9 1.0
C11 A:KLN1500 1.7 37.2 1.0
C12 A:KLN1500 2.7 37.8 1.0
C10 A:KLN1500 2.7 36.8 1.0
CD2 A:LEU210 3.5 60.6 1.0
CG A:LEU210 3.6 60.4 1.0
CE2 A:PHE241 3.8 43.2 1.0
C26 A:KLN1501 3.9 63.4 1.0
C13 A:KLN1500 4.0 37.5 1.0
C9 A:KLN1500 4.0 37.3 1.0
CG A:PHE304 4.4 25.2 1.0
CD2 A:PHE304 4.4 24.9 1.0
CD2 A:PHE241 4.4 43.8 1.0
CB A:LEU210 4.5 60.7 1.0
C8 A:KLN1500 4.5 36.5 1.0
CZ A:PHE241 4.5 43.3 1.0
CD1 A:PHE304 4.6 24.3 1.0
CE2 A:PHE304 4.6 25.2 1.0
C25 A:KLN1501 4.7 63.7 1.0
O A:LEU210 4.7 61.2 1.0
CD1 A:LEU210 4.7 60.2 1.0
CB A:PHE304 4.8 25.7 1.0
CE1 A:PHE304 4.8 24.7 1.0
CZ A:PHE304 4.8 24.9 1.0
CD2 A:LEU211 4.9 63.4 1.0
C22 A:KLN1501 4.9 64.6 1.0
C A:LEU210 4.9 61.2 1.0

Chlorine binding site 2 out of 10 in 2v0m

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Chlorine binding site 2 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1500

b:38.8
occ:1.00
 CL2 A:KLN1500 0.0 38.8 1.0
C9 A:KLN1500 1.7 37.3 1.0
C10 A:KLN1500 2.7 36.8 1.0
C8 A:KLN1500 2.7 36.5 1.0
O1 A:KLN1500 2.8 33.5 1.0
C5 A:KLN1500 3.1 35.0 1.0
C4 A:KLN1500 3.4 33.2 1.0
CD1 A:LEU482 3.8 52.4 1.0
C24 A:KLN1501 3.9 64.9 1.0
CD2 A:LEU482 3.9 52.4 1.0
CG A:LEU482 4.0 52.8 1.0
C11 A:KLN1500 4.0 37.2 1.0
C6 A:KLN1500 4.0 33.0 1.0
C13 A:KLN1500 4.0 37.5 1.0
N1 A:KLN1500 4.1 32.4 1.0
C3 A:KLN1500 4.2 32.4 1.0
CE2 A:PHE304 4.4 25.2 1.0
C19 A:KLN1501 4.4 66.5 1.0
O2 A:KLN1500 4.5 34.1 1.0
C23 A:KLN1501 4.5 64.2 1.0
C12 A:KLN1500 4.5 37.8 1.0
C20 A:KLN1500 4.6 32.5 1.0
CD2 A:LEU211 4.6 63.4 1.0
C21 A:KLN1501 4.6 65.0 1.0
N3 A:KLN1501 4.8 65.9 1.0
N4 A:KLN1501 4.8 63.9 1.0
CD2 A:PHE304 4.8 24.9 1.0
CD1 A:LEU211 4.9 63.6 1.0
C14 A:KLN1500 4.9 32.9 1.0
C19 A:KLN1500 5.0 32.7 1.0

Chlorine binding site 3 out of 10 in 2v0m

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Chlorine binding site 3 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1501

b:78.5
occ:1.00
 CL1 A:KLN1501 0.0 78.5 1.0
C11 A:KLN1501 1.7 77.9 1.0
C10 A:KLN1501 2.7 78.0 1.0
C12 A:KLN1501 2.7 77.7 1.0
N A:LEU216 2.9 58.9 1.0
CA A:LEU216 3.1 57.6 1.0
CD1 A:LEU221 3.5 42.9 1.0
CB A:LEU221 3.7 42.9 1.0
C A:LEU216 3.9 56.6 1.0
C9 A:KLN1501 4.0 78.0 1.0
C13 A:KLN1501 4.0 77.8 1.0
CD2 A:LEU216 4.0 58.4 1.0
C A:PHE215 4.0 60.2 1.0
N A:ASP217 4.0 55.2 1.0
CG A:LEU221 4.1 43.0 1.0
CA A:LEU221 4.1 42.9 1.0
N A:LEU221 4.3 43.4 1.0
CB A:LEU216 4.4 57.8 1.0
CD2 A:LEU221 4.4 43.1 1.0
CA A:PHE215 4.5 61.1 1.0
C8 A:KLN1501 4.5 77.6 1.0
O A:ASP217 4.5 53.0 1.0
CG A:LEU216 4.7 58.0 1.0
O A:LEU216 4.9 56.4 1.0
O A:ASP214 5.0 62.5 1.0

Chlorine binding site 4 out of 10 in 2v0m

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Chlorine binding site 4 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1501

b:78.1
occ:1.00
 CL2 A:KLN1501 0.0 78.1 1.0
C9 A:KLN1501 1.7 78.0 1.0
C10 A:KLN1501 2.6 78.0 1.0
C6 A:KLN1501 2.7 73.9 1.0
C8 A:KLN1501 2.8 77.6 1.0
O1 A:KLN1501 2.9 75.6 1.0
C5 A:KLN1501 3.2 77.0 1.0
CE1 A:PHE213 3.5 65.3 1.0
O2 A:KLN1501 3.5 76.2 1.0
CD1 A:PHE213 3.5 65.2 1.0
C14 A:KLN1501 3.6 71.4 1.0
C7 A:KLN1501 3.7 75.0 1.0
O A:ASP214 3.8 62.5 1.0
C11 A:KLN1501 3.9 77.9 1.0
C13 A:KLN1501 4.0 77.8 1.0
CZ A:PHE57 4.5 38.6 1.0
C12 A:KLN1501 4.5 77.7 1.0
CZ A:PHE213 4.6 65.3 1.0
CG A:PHE213 4.7 64.7 1.0
C A:ASP214 4.7 62.5 1.0
C4 A:KLN1501 4.7 77.2 1.0
O3 A:KLN1501 4.7 67.8 1.0
CB A:PHE220 5.0 44.7 1.0

Chlorine binding site 5 out of 10 in 2v0m

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Chlorine binding site 5 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1498

b:36.6
occ:1.00
 CL1 B:KLN1498 0.0 36.6 1.0
C11 B:KLN1498 1.7 35.4 1.0
C10 B:KLN1498 2.7 35.3 1.0
C12 B:KLN1498 2.7 35.8 1.0
CE2 B:PHE241 3.4 45.7 1.0
CD2 B:LEU210 3.5 60.3 1.0
CG B:LEU210 3.6 60.5 1.0
C26 B:KLN1499 3.9 36.7 1.0
C9 B:KLN1498 4.0 35.7 1.0
C13 B:KLN1498 4.0 35.6 1.0
O B:LEU210 4.0 61.2 1.0
CD2 B:PHE241 4.1 46.0 1.0
CD2 B:LEU211 4.2 63.2 1.0
CZ B:PHE241 4.3 45.6 1.0
CB B:LEU210 4.4 60.4 1.0
CG B:LEU211 4.4 63.2 1.0
C8 B:KLN1498 4.5 34.5 1.0
CG B:PHE304 4.6 21.6 1.0
C25 B:KLN1499 4.7 36.8 1.0
C B:LEU210 4.7 61.1 1.0
CD1 B:PHE304 4.7 21.5 1.0
CD2 B:PHE304 4.8 21.7 1.0
CD1 B:LEU210 4.8 60.3 1.0
C22 B:KLN1499 5.0 38.1 1.0
CE1 B:PHE304 5.0 21.6 1.0

Chlorine binding site 6 out of 10 in 2v0m

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Chlorine binding site 6 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1498

b:37.1
occ:1.00
 CL2 B:KLN1498 0.0 37.1 1.0
C9 B:KLN1498 1.7 35.7 1.0
C10 B:KLN1498 2.7 35.3 1.0
C8 B:KLN1498 2.7 34.5 1.0
O1 B:KLN1498 2.9 31.1 1.0
C5 B:KLN1498 3.1 33.0 1.0
C4 B:KLN1498 3.2 30.3 1.0
CD1 B:LEU482 3.4 53.8 1.0
C11 B:KLN1498 4.0 35.4 1.0
N1 B:KLN1498 4.0 28.6 1.0
C13 B:KLN1498 4.0 35.6 1.0
C3 B:KLN1498 4.0 27.4 1.0
CD2 B:LEU482 4.1 53.3 1.0
CE2 B:PHE304 4.1 21.7 1.0
CG B:LEU482 4.1 54.0 1.0
C24 B:KLN1499 4.2 39.1 1.0
CD1 B:LEU211 4.2 63.1 1.0
C6 B:KLN1498 4.2 31.6 1.0
O2 B:KLN1498 4.5 32.6 1.0
C12 B:KLN1498 4.5 35.8 1.0
C23 B:KLN1499 4.5 38.1 1.0
CD2 B:PHE304 4.6 21.7 1.0
N4 B:KLN1499 4.8 37.3 1.0
C21 B:KLN1499 4.9 38.9 1.0
CZ B:PHE304 5.0 21.3 1.0

Chlorine binding site 7 out of 10 in 2v0m

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Chlorine binding site 7 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1498

b:31.2
occ:1.00
 CL1 C:KLN1498 0.0 31.2 1.0
C11 C:KLN1498 1.7 31.1 1.0
C12 C:KLN1498 2.7 31.8 1.0
C10 C:KLN1498 2.7 30.7 1.0
CE2 C:PHE241 3.3 42.5 1.0
C26 C:KLN1499 3.6 55.6 1.0
CD2 C:LEU210 3.6 37.9 1.0
CZ C:PHE241 3.8 43.1 1.0
CG C:LEU210 3.8 38.0 1.0
CD2 C:LEU211 3.8 38.6 1.0
C13 C:KLN1498 4.0 31.2 1.0
C9 C:KLN1498 4.0 30.7 1.0
CD2 C:PHE241 4.2 43.2 1.0
C25 C:KLN1499 4.4 55.6 1.0
C8 C:KLN1498 4.5 30.1 1.0
CG C:LEU211 4.6 38.7 1.0
CD2 C:PHE304 4.6 15.4 1.0
O C:LEU210 4.6 38.2 1.0
CG C:PHE304 4.7 14.8 1.0
CB C:LEU210 4.7 38.1 1.0
CD1 C:LEU210 4.8 37.4 1.0
CE2 C:PHE304 4.9 15.6 1.0
O4 C:KLN1499 4.9 55.5 1.0
N4 C:KLN1499 4.9 55.7 1.0
CE1 C:PHE241 4.9 43.2 1.0
C22 C:KLN1499 5.0 56.0 1.0
CD1 C:PHE304 5.0 14.6 1.0

Chlorine binding site 8 out of 10 in 2v0m

Go back to Chlorine Binding Sites List in 2v0m
Chlorine binding site 8 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


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 Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1498

b:32.1
occ:1.00
 CL2 C:KLN1498 0.0 32.1 1.0
C9 C:KLN1498 1.7 30.7 1.0
C10 C:KLN1498 2.7 30.7 1.0
C8 C:KLN1498 2.8 30.1 1.0
O1 C:KLN1498 3.0 28.2 1.0
C5 C:KLN1498 3.2 29.0 1.0
C4 C:KLN1498 3.4 27.1 1.0
C24 C:KLN1499 4.0 56.7 1.0
C11 C:KLN1498 4.0 31.1 1.0
CE2 C:PHE304 4.0 15.6 1.0
C13 C:KLN1498 4.0 31.2 1.0
C6 C:KLN1498 4.3 29.1 1.0
CG C:LEU482 4.3 42.5 1.0
N1 C:KLN1498 4.3 25.7 1.0
CD1 C:LEU482 4.4 41.3 1.0
CD2 C:LEU482 4.4 42.3 1.0
C3 C:KLN1498 4.4 25.4 1.0
C12 C:KLN1498 4.5 31.8 1.0
C23 C:KLN1499 4.5 56.1 1.0
O2 C:KLN1498 4.6 28.6 1.0
CD2 C:PHE304 4.6 15.4 1.0
C19 C:KLN1499 4.7 58.4 1.0
CD1 C:LEU211 4.7 38.5 1.0
CG C:LEU211 4.8 38.7 1.0
N4 C:KLN1499 4.9 55.7 1.0
CZ C:PHE304 4.9 15.8 1.0
C20 C:KLN1498 4.9 32.8 1.0
N3 C:KLN1499 5.0 57.6 1.0
C21 C:KLN1499 5.0 56.5 1.0

Chlorine binding site 9 out of 10 in 2v0m

Go back to Chlorine Binding Sites List in 2v0m
Chlorine binding site 9 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1498

b:27.9
occ:1.00
 CL1 D:KLN1498 0.0 27.9 1.0
C11 D:KLN1498 1.7 27.1 1.0
C10 D:KLN1498 2.7 26.7 1.0
C12 D:KLN1498 2.7 27.1 1.0
CD2 D:LEU210 3.5 48.9 1.0
CG D:LEU210 3.5 48.7 1.0
CE2 D:PHE241 3.6 45.4 1.0
C26 D:KLN1499 3.9 55.0 1.0
C9 D:KLN1498 4.0 26.8 1.0
C13 D:KLN1498 4.0 27.1 1.0
CZ D:PHE241 4.2 45.3 1.0
O D:LEU210 4.2 50.4 1.0
CD2 D:PHE241 4.3 45.1 1.0
CD1 D:LEU211 4.3 53.3 1.0
CB D:LEU210 4.5 48.9 1.0
C8 D:KLN1498 4.5 26.3 1.0
CD1 D:LEU210 4.5 48.2 1.0
CG D:PHE304 4.6 13.0 1.0
CD2 D:PHE304 4.6 13.0 1.0
C25 D:KLN1499 4.8 55.3 1.0
C D:LEU210 4.8 50.2 1.0
CD1 D:PHE304 4.8 13.2 1.0
CE2 D:PHE304 4.9 13.2 1.0
C22 D:KLN1499 4.9 56.3 1.0
CB D:PHE304 5.0 13.3 1.0

Chlorine binding site 10 out of 10 in 2v0m

Go back to Chlorine Binding Sites List in 2v0m
Chlorine binding site 10 out of 10 in the Crystal Structure of Human P450 3A4 in Complex with Ketoconazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Human P450 3A4 in Complex with Ketoconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1498

b:28.3
occ:1.00
 CL2 D:KLN1498 0.0 28.3 1.0
C9 D:KLN1498 1.7 26.8 1.0
C10 D:KLN1498 2.7 26.7 1.0
C8 D:KLN1498 2.8 26.3 1.0
O1 D:KLN1498 3.0 24.1 1.0
C5 D:KLN1498 3.2 25.1 1.0
C4 D:KLN1498 3.4 23.0 1.0
C11 D:KLN1498 4.0 27.1 1.0
C13 D:KLN1498 4.0 27.1 1.0
CD1 D:LEU482 4.1 40.9 1.0
CE2 D:PHE304 4.1 13.2 1.0
C24 D:KLN1499 4.1 57.6 1.0
C6 D:KLN1498 4.2 24.2 1.0
N1 D:KLN1498 4.2 21.0 1.0
CG D:LEU482 4.3 41.2 1.0
C3 D:KLN1498 4.3 20.0 1.0
CD2 D:LEU482 4.4 40.9 1.0
C12 D:KLN1498 4.5 27.1 1.0
CD2 D:LEU211 4.5 52.8 1.0
O2 D:KLN1498 4.6 24.1 1.0
C23 D:KLN1499 4.6 56.7 1.0
C21 D:KLN1499 4.6 57.5 1.0
CD2 D:PHE304 4.6 13.0 1.0
N4 D:KLN1499 4.7 56.0 1.0
C20 D:KLN1498 4.9 24.6 1.0
C19 D:KLN1499 4.9 59.5 1.0
N3 D:KLN1499 4.9 58.8 1.0

Reference:

M.Ekroos, T.Sjogren. Structural Basis For Ligand Promiscuity in Cytochrome P450 3A4 Proc.Natl.Acad.Sci.Usa V. 103 13682 2006.
ISSN: ISSN 0027-8424
PubMed: 16954191
DOI: 10.1073/PNAS.0603236103
Page generated: Sat Jul 20 11:30:17 2024

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