Fluorine in PDB 6udm: Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
Enzymatic activity of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
All present enzymatic activity of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726:
1.14.14.1;
4.2.1.152;
Protein crystallography data
The structure of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726, PDB code: 6udm
was solved by
A.G.Bart,
E.E.Scott,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.64 /
3.08
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
241.281,
241.281,
125.298,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
20.9 /
22.1
|
Other elements in 6udm:
The structure of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
(pdb code 6udm). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726, PDB code: 6udm:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6udm
Go back to
Fluorine Binding Sites List in 6udm
Fluorine binding site 1 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F602
b:71.4
occ:1.00
|
F14
|
A:Q4P602
|
0.0
|
71.4
|
1.0
|
|
C13
|
A:Q4P602
|
1.4
|
68.6
|
1.0
|
|
C12
|
A:Q4P602
|
2.4
|
68.3
|
1.0
|
|
C15
|
A:Q4P602
|
2.4
|
69.4
|
1.0
|
|
H121
|
A:Q4P602
|
2.5
|
68.3
|
1.0
|
|
H151
|
A:Q4P602
|
2.6
|
69.4
|
1.0
|
|
HG21
|
A:THR321
|
2.6
|
82.0
|
1.0
|
|
HG22
|
A:VAL382
|
2.7
|
72.5
|
1.0
|
|
HG21
|
A:VAL382
|
2.7
|
72.5
|
1.0
|
|
HG12
|
A:VAL382
|
2.8
|
71.9
|
1.0
|
|
HG23
|
A:THR497
|
2.9
|
79.6
|
1.0
|
|
HG22
|
A:THR497
|
2.9
|
79.6
|
1.0
|
|
HG23
|
A:THR321
|
2.9
|
82.0
|
1.0
|
|
CG2
|
A:VAL382
|
3.1
|
60.4
|
1.0
|
|
CG2
|
A:THR321
|
3.2
|
68.3
|
1.0
|
|
CG2
|
A:THR497
|
3.2
|
66.4
|
1.0
|
|
HG21
|
A:THR497
|
3.4
|
79.6
|
1.0
|
|
HG
|
A:LEU496
|
3.6
|
78.2
|
1.0
|
|
C11
|
A:Q4P602
|
3.6
|
69.3
|
1.0
|
|
C09
|
A:Q4P602
|
3.7
|
70.4
|
1.0
|
|
CG1
|
A:VAL382
|
3.7
|
59.9
|
1.0
|
|
HG22
|
A:THR321
|
3.7
|
82.0
|
1.0
|
|
HG23
|
A:VAL382
|
3.9
|
72.5
|
1.0
|
|
CB
|
A:VAL382
|
4.0
|
58.8
|
1.0
|
|
HG11
|
A:VAL382
|
4.1
|
71.9
|
1.0
|
|
C10
|
A:Q4P602
|
4.1
|
70.4
|
1.0
|
|
O
|
A:LEU496
|
4.2
|
61.5
|
1.0
|
|
CHB
|
A:HEM601
|
4.2
|
64.0
|
1.0
|
|
HB
|
A:THR321
|
4.3
|
80.5
|
1.0
|
|
HG13
|
A:VAL382
|
4.3
|
71.9
|
1.0
|
|
H111
|
A:Q4P602
|
4.4
|
69.3
|
1.0
|
|
CB
|
A:THR321
|
4.4
|
67.1
|
1.0
|
|
C1B
|
A:HEM601
|
4.4
|
64.3
|
1.0
|
|
C4A
|
A:HEM601
|
4.4
|
64.3
|
1.0
|
|
HHB
|
A:HEM601
|
4.5
|
64.0
|
1.0
|
|
CG
|
A:LEU496
|
4.5
|
65.2
|
1.0
|
|
HD11
|
A:LEU496
|
4.5
|
76.6
|
1.0
|
|
HMB
|
A:HEM601
|
4.5
|
63.1
|
1.0
|
|
HE1
|
A:PHE381
|
4.6
|
74.1
|
1.0
|
|
HA
|
A:THR497
|
4.6
|
76.0
|
1.0
|
|
CB
|
A:THR497
|
4.7
|
65.9
|
1.0
|
|
HD22
|
A:LEU496
|
4.7
|
81.9
|
1.0
|
|
HD12
|
A:LEU496
|
4.7
|
76.6
|
1.0
|
|
HB
|
A:VAL382
|
4.7
|
70.5
|
1.0
|
|
HA
|
A:VAL382
|
4.7
|
69.6
|
1.0
|
|
C
|
A:LEU496
|
4.8
|
62.9
|
1.0
|
|
HA
|
A:THR321
|
4.8
|
81.2
|
1.0
|
|
CD1
|
A:LEU496
|
4.8
|
63.8
|
1.0
|
|
HMAA
|
A:HEM601
|
4.8
|
63.2
|
1.0
|
|
C2B
|
A:HEM601
|
4.8
|
63.4
|
1.0
|
|
C3A
|
A:HEM601
|
4.8
|
64.2
|
1.0
|
|
NB
|
A:HEM601
|
4.9
|
64.2
|
1.0
|
|
NA
|
A:HEM601
|
4.9
|
65.3
|
1.0
|
|
HMA
|
A:HEM601
|
5.0
|
63.2
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 6udm
Go back to
Fluorine Binding Sites List in 6udm
Fluorine binding site 2 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F602
b:77.2
occ:1.00
|
F14
|
B:Q4P602
|
0.0
|
77.2
|
1.0
|
|
C13
|
B:Q4P602
|
1.4
|
71.7
|
1.0
|
|
C12
|
B:Q4P602
|
2.4
|
71.0
|
1.0
|
|
C15
|
B:Q4P602
|
2.4
|
70.7
|
1.0
|
|
H121
|
B:Q4P602
|
2.5
|
71.0
|
1.0
|
|
H151
|
B:Q4P602
|
2.6
|
70.7
|
1.0
|
|
HG21
|
B:VAL382
|
2.6
|
75.2
|
1.0
|
|
HG22
|
B:THR321
|
2.7
|
82.8
|
1.0
|
|
HG22
|
B:VAL382
|
2.7
|
75.2
|
1.0
|
|
HG22
|
B:THR497
|
2.8
|
81.6
|
1.0
|
|
HG23
|
B:THR497
|
2.9
|
81.6
|
1.0
|
|
HG21
|
B:THR321
|
3.0
|
82.8
|
1.0
|
|
CG2
|
B:VAL382
|
3.1
|
62.6
|
1.0
|
|
CG2
|
B:THR497
|
3.2
|
68.0
|
1.0
|
|
CG2
|
B:THR321
|
3.3
|
69.0
|
1.0
|
|
HG11
|
B:VAL382
|
3.3
|
73.7
|
1.0
|
|
HG13
|
B:VAL382
|
3.4
|
73.7
|
1.0
|
|
HG21
|
B:THR497
|
3.4
|
81.6
|
1.0
|
|
C11
|
B:Q4P602
|
3.6
|
70.4
|
1.0
|
|
C09
|
B:Q4P602
|
3.7
|
69.3
|
1.0
|
|
HG
|
B:LEU496
|
3.7
|
81.8
|
1.0
|
|
CG1
|
B:VAL382
|
3.7
|
61.4
|
1.0
|
|
HG23
|
B:VAL382
|
3.8
|
75.2
|
1.0
|
|
HG23
|
B:THR321
|
3.9
|
82.8
|
1.0
|
|
CB
|
B:VAL382
|
4.0
|
61.0
|
1.0
|
|
CHB
|
B:HEM601
|
4.1
|
67.5
|
1.0
|
|
C10
|
B:Q4P602
|
4.1
|
69.7
|
1.0
|
|
O
|
B:LEU496
|
4.2
|
64.2
|
1.0
|
|
HB
|
B:THR321
|
4.2
|
80.0
|
1.0
|
|
C1B
|
B:HEM601
|
4.3
|
68.0
|
1.0
|
|
HHB
|
B:HEM601
|
4.3
|
67.5
|
1.0
|
|
CB
|
B:THR321
|
4.4
|
66.7
|
1.0
|
|
H111
|
B:Q4P602
|
4.4
|
70.4
|
1.0
|
|
C4A
|
B:HEM601
|
4.4
|
68.5
|
1.0
|
|
HMB
|
B:HEM601
|
4.4
|
64.1
|
1.0
|
|
CG
|
B:LEU496
|
4.6
|
68.2
|
1.0
|
|
HD11
|
B:LEU496
|
4.6
|
81.0
|
1.0
|
|
HG12
|
B:VAL382
|
4.6
|
73.7
|
1.0
|
|
HA
|
B:THR497
|
4.6
|
76.6
|
1.0
|
|
HE2
|
B:PHE381
|
4.7
|
73.8
|
1.0
|
|
C2B
|
B:HEM601
|
4.7
|
65.9
|
1.0
|
|
CB
|
B:THR497
|
4.7
|
66.4
|
1.0
|
|
HB
|
B:VAL382
|
4.7
|
73.3
|
1.0
|
|
HA
|
B:VAL382
|
4.7
|
72.1
|
1.0
|
|
HD12
|
B:LEU496
|
4.7
|
81.0
|
1.0
|
|
HA
|
B:THR321
|
4.7
|
80.4
|
1.0
|
|
HD23
|
B:LEU496
|
4.8
|
83.1
|
1.0
|
|
NB
|
B:HEM601
|
4.8
|
68.7
|
1.0
|
|
C
|
B:LEU496
|
4.8
|
64.9
|
1.0
|
|
CD1
|
B:LEU496
|
4.9
|
67.5
|
1.0
|
|
HMAA
|
B:HEM601
|
4.9
|
64.2
|
1.0
|
|
NA
|
B:HEM601
|
4.9
|
70.1
|
1.0
|
|
CMB
|
B:HEM601
|
4.9
|
64.1
|
1.0
|
|
C3A
|
B:HEM601
|
4.9
|
66.1
|
1.0
|
|
CA
|
B:VAL382
|
5.0
|
60.1
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6udm
Go back to
Fluorine Binding Sites List in 6udm
Fluorine binding site 3 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F602
b:77.8
occ:1.00
|
F14
|
C:Q4P602
|
0.0
|
77.8
|
1.0
|
|
C13
|
C:Q4P602
|
1.4
|
71.3
|
1.0
|
|
C12
|
C:Q4P602
|
2.2
|
68.4
|
1.0
|
|
C15
|
C:Q4P602
|
2.4
|
71.0
|
1.0
|
|
H121
|
C:Q4P602
|
2.4
|
68.4
|
1.0
|
|
H151
|
C:Q4P602
|
2.6
|
71.0
|
1.0
|
|
HG23
|
C:VAL382
|
2.9
|
76.7
|
1.0
|
|
HG23
|
C:THR321
|
3.0
|
80.2
|
1.0
|
|
HG22
|
C:THR321
|
3.1
|
80.2
|
1.0
|
|
HG11
|
C:VAL382
|
3.4
|
79.0
|
1.0
|
|
C11
|
C:Q4P602
|
3.4
|
68.6
|
1.0
|
|
HG22
|
C:THR497
|
3.5
|
81.2
|
1.0
|
|
HG13
|
C:VAL382
|
3.5
|
79.0
|
1.0
|
|
CG2
|
C:THR321
|
3.5
|
66.8
|
1.0
|
|
HG
|
C:LEU496
|
3.6
|
83.9
|
1.0
|
|
HG21
|
C:THR497
|
3.6
|
81.2
|
1.0
|
|
C09
|
C:Q4P602
|
3.6
|
70.2
|
1.0
|
|
CG2
|
C:VAL382
|
3.8
|
63.9
|
1.0
|
|
CG1
|
C:VAL382
|
3.9
|
65.8
|
1.0
|
|
CG2
|
C:THR497
|
3.9
|
67.7
|
1.0
|
|
CHB
|
C:HEM601
|
3.9
|
63.0
|
1.0
|
|
C10
|
C:Q4P602
|
4.0
|
70.8
|
1.0
|
|
HG21
|
C:THR321
|
4.0
|
80.2
|
1.0
|
|
C4A
|
C:HEM601
|
4.0
|
63.2
|
1.0
|
|
HG21
|
C:VAL382
|
4.0
|
76.7
|
1.0
|
|
HD12
|
C:LEU496
|
4.1
|
84.7
|
1.0
|
|
HG23
|
C:THR497
|
4.1
|
81.2
|
1.0
|
|
H111
|
C:Q4P602
|
4.2
|
68.6
|
1.0
|
|
HD21
|
C:LEU496
|
4.2
|
85.0
|
1.0
|
|
C1B
|
C:HEM601
|
4.2
|
63.0
|
1.0
|
|
HHB
|
C:HEM601
|
4.2
|
63.0
|
1.0
|
|
CG
|
C:LEU496
|
4.4
|
69.9
|
1.0
|
|
HG22
|
C:VAL382
|
4.4
|
76.7
|
1.0
|
|
NA
|
C:HEM601
|
4.4
|
63.6
|
1.0
|
|
C3A
|
C:HEM601
|
4.4
|
64.2
|
1.0
|
|
CB
|
C:VAL382
|
4.5
|
64.3
|
1.0
|
|
O
|
C:LEU496
|
4.6
|
66.4
|
1.0
|
|
CD1
|
C:LEU496
|
4.6
|
70.5
|
1.0
|
|
HMB
|
C:HEM601
|
4.6
|
62.4
|
1.0
|
|
HD13
|
C:LEU496
|
4.6
|
84.7
|
1.0
|
|
HMAA
|
C:HEM601
|
4.6
|
64.8
|
1.0
|
|
NB
|
C:HEM601
|
4.7
|
62.5
|
1.0
|
|
HB
|
C:THR321
|
4.7
|
78.8
|
1.0
|
|
HG12
|
C:VAL382
|
4.7
|
79.0
|
1.0
|
|
CD2
|
C:LEU496
|
4.7
|
70.8
|
1.0
|
|
HMA
|
C:HEM601
|
4.7
|
64.8
|
1.0
|
|
HD13
|
C:ILE386
|
4.8
|
84.3
|
1.0
|
|
CB
|
C:THR321
|
4.8
|
65.7
|
1.0
|
|
C2B
|
C:HEM601
|
4.8
|
61.9
|
1.0
|
|
CMA
|
C:HEM601
|
4.9
|
64.8
|
1.0
|
|
HD23
|
C:LEU496
|
4.9
|
85.0
|
1.0
|
|
C08
|
C:Q4P602
|
4.9
|
69.7
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 6udm
Go back to
Fluorine Binding Sites List in 6udm
Fluorine binding site 4 out
of 4 in the Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) Ict-2726 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F602
b:84.7
occ:1.00
|
F14
|
D:Q4P602
|
0.0
|
84.7
|
1.0
|
|
C13
|
D:Q4P602
|
1.4
|
79.3
|
1.0
|
|
C15
|
D:Q4P602
|
2.4
|
80.3
|
1.0
|
|
C12
|
D:Q4P602
|
2.4
|
76.7
|
1.0
|
|
H121
|
D:Q4P602
|
2.5
|
76.7
|
1.0
|
|
HG21
|
D:VAL382
|
2.6
|
80.1
|
1.0
|
|
H151
|
D:Q4P602
|
2.6
|
80.3
|
1.0
|
|
HG22
|
D:VAL382
|
2.7
|
80.1
|
1.0
|
|
HG22
|
D:THR321
|
2.8
|
89.9
|
1.0
|
|
HG22
|
D:THR497
|
2.9
|
88.8
|
1.0
|
|
CG2
|
D:VAL382
|
3.1
|
66.8
|
1.0
|
|
HG23
|
D:THR497
|
3.1
|
88.8
|
1.0
|
|
HG21
|
D:THR321
|
3.1
|
89.9
|
1.0
|
|
HG11
|
D:VAL382
|
3.1
|
80.8
|
1.0
|
|
CG2
|
D:THR497
|
3.3
|
74.0
|
1.0
|
|
HG13
|
D:VAL382
|
3.4
|
80.8
|
1.0
|
|
CG2
|
D:THR321
|
3.4
|
75.0
|
1.0
|
|
HG21
|
D:THR497
|
3.5
|
88.8
|
1.0
|
|
CG1
|
D:VAL382
|
3.6
|
67.4
|
1.0
|
|
C11
|
D:Q4P602
|
3.6
|
77.3
|
1.0
|
|
C09
|
D:Q4P602
|
3.7
|
80.5
|
1.0
|
|
HG
|
D:LEU496
|
3.8
|
93.8
|
1.0
|
|
HG23
|
D:VAL382
|
3.8
|
80.1
|
1.0
|
|
CB
|
D:VAL382
|
3.9
|
66.5
|
1.0
|
|
CHB
|
D:HEM601
|
4.0
|
68.8
|
1.0
|
|
HG23
|
D:THR321
|
4.0
|
89.9
|
1.0
|
|
C10
|
D:Q4P602
|
4.1
|
80.1
|
1.0
|
|
HHB
|
D:HEM601
|
4.1
|
68.8
|
1.0
|
|
C1B
|
D:HEM601
|
4.2
|
69.0
|
1.0
|
|
HB
|
D:THR321
|
4.3
|
88.2
|
1.0
|
|
C4A
|
D:HEM601
|
4.3
|
68.8
|
1.0
|
|
O
|
D:LEU496
|
4.3
|
72.3
|
1.0
|
|
HMB
|
D:HEM601
|
4.4
|
65.9
|
1.0
|
|
H111
|
D:Q4P602
|
4.4
|
77.3
|
1.0
|
|
CB
|
D:THR321
|
4.5
|
73.5
|
1.0
|
|
HG12
|
D:VAL382
|
4.5
|
80.8
|
1.0
|
|
HB
|
D:VAL382
|
4.5
|
79.8
|
1.0
|
|
HMAA
|
D:HEM601
|
4.6
|
68.4
|
1.0
|
|
C2B
|
D:HEM601
|
4.6
|
67.8
|
1.0
|
|
HA
|
D:THR497
|
4.7
|
85.3
|
1.0
|
|
CG
|
D:LEU496
|
4.7
|
78.2
|
1.0
|
|
HE1
|
D:PHE381
|
4.7
|
80.9
|
1.0
|
|
CB
|
D:THR497
|
4.8
|
72.4
|
1.0
|
|
NB
|
D:HEM601
|
4.8
|
68.5
|
1.0
|
|
C3A
|
D:HEM601
|
4.8
|
69.0
|
1.0
|
|
HA
|
D:VAL382
|
4.8
|
78.9
|
1.0
|
|
HD11
|
D:LEU496
|
4.8
|
92.0
|
1.0
|
|
HD23
|
D:LEU496
|
4.8
|
95.3
|
1.0
|
|
NA
|
D:HEM601
|
4.9
|
69.4
|
1.0
|
|
CMB
|
D:HEM601
|
4.9
|
65.9
|
1.0
|
|
HA
|
D:THR321
|
4.9
|
89.7
|
1.0
|
|
HMA
|
D:HEM601
|
4.9
|
68.4
|
1.0
|
|
C
|
D:LEU496
|
5.0
|
73.2
|
1.0
|
|
HD12
|
D:LEU496
|
5.0
|
92.0
|
1.0
|
|
Reference:
A.G.Bart,
E.E.Scott.
Designed Duocarmycin Prodrugs For Human Cytochrome P450 1A1 and 2W1 To Be Published.
Page generated: Sun Dec 13 13:17:22 2020
|
