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Iodine in PDB 5bvo: Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors

Enzymatic activity of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors

All present enzymatic activity of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors:
2.7.10.1;

Protein crystallography data

The structure of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors, PDB code: 5bvo was solved by C.Murray, V.Berdini, I.Buck, M.Carr, A.Cleasby, J.Coyle, J.Curry, J.Day, K.Hearn, A.Iqbal, L.Lee, V.Martins, P.Mortenson, J.Munck, L.Page, S.Patel, S.Roomans, T.Kirsten, G.Saxty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.58 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.921, 78.360, 75.732, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.6

Other elements in 5bvo:

The structure of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors also contains other interesting chemical elements:

Fluorine (F) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors (pdb code 5bvo). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors, PDB code: 5bvo:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 5bvo

Go back to Iodine Binding Sites List in 5bvo
Iodine binding site 1 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:34.0
occ:1.00
 O A:HOH1222 3.4 26.1 1.0
CA A:PHE845 3.9 32.4 1.0
N A:GLN847 4.0 31.6 1.0
C A:PHE845 4.0 31.4 1.0
CB A:GLN847 4.1 35.4 1.0
CG A:LEU848 4.3 35.7 1.0
N A:GLY846 4.3 32.0 1.0
CA A:GLN847 4.5 33.8 1.0
O A:PHE845 4.5 32.5 1.0
CD2 A:LEU848 4.6 37.2 1.0
CG A:GLN847 4.7 38.0 1.0
CD1 A:PHE845 4.7 34.3 1.0
N A:LEU848 4.7 34.4 1.0
N A:PHE845 4.8 28.8 1.0
O A:HOH1142 4.8 35.1 1.0
C A:GLN847 4.8 35.0 1.0
CB A:PHE845 4.9 29.5 1.0
O A:HOH1172 4.9 37.3 1.0
CD1 A:LEU848 4.9 39.0 1.0

Iodine binding site 2 out of 7 in 5bvo

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Iodine binding site 2 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:52.7
occ:1.00
 OE1 A:GLN900 2.9 51.6 1.0
O A:HOH1305 3.1 50.7 1.0
CD1 A:LEU883 3.7 42.0 1.0
CD A:GLN900 3.8 54.8 1.0
NH2 A:ARG886 3.8 41.4 1.0
NE A:ARG886 3.8 43.5 1.0
CG A:GLN900 3.8 51.1 1.0
CG A:PRO896 4.1 38.4 1.0
CB A:PRO896 4.1 37.2 1.0
O A:GLN900 4.1 39.8 1.0
CG A:LEU883 4.2 41.0 1.0
CZ A:ARG886 4.2 44.7 1.0
CD2 A:LEU901 4.3 30.6 1.0
CB A:PHE904 4.3 37.9 1.0
C A:GLN900 4.4 40.8 1.0
CD1 A:PHE904 4.6 42.5 1.0
N A:LEU901 4.6 35.8 1.0
CA A:LEU901 4.6 34.7 1.0
CG A:PHE904 4.6 39.9 1.0
CB A:GLN900 4.7 46.0 1.0
CB A:LEU883 4.9 38.6 1.0
CD A:ARG886 4.9 41.3 1.0
CG A:LEU901 4.9 30.1 1.0

Iodine binding site 3 out of 7 in 5bvo

Go back to Iodine Binding Sites List in 5bvo
Iodine binding site 3 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:0.8
occ:1.00
 O A:GLY622 3.3 71.4 1.0
CG2 A:VAL624 3.6 51.2 1.0
C A:GLU618 3.9 71.8 1.0
I A:IOD1007 4.0 69.5 1.0
CE A:LYS655 4.1 45.2 1.0
O A:GLU618 4.1 71.5 1.0
CD A:LYS655 4.4 42.7 1.0
CD2 A:PHE785 4.4 36.8 1.0
NZ A:LYS655 4.4 45.1 1.0
C A:GLY622 4.5 68.6 1.0
CA A:GLU618 4.6 75.5 1.0
CG A:LYS655 4.6 42.4 1.0
CE2 A:PHE785 4.9 40.1 1.0
CB A:VAL624 4.9 48.1 1.0
H36 A:4VE1008 4.9 33.3 0.9
N A:GLU618 5.0 72.6 1.0

Iodine binding site 4 out of 7 in 5bvo

Go back to Iodine Binding Sites List in 5bvo
Iodine binding site 4 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:0.6
occ:1.00
 O A:HOH1307 2.5 54.8 1.0
NH1 A:ARG686 3.3 75.3 1.0
C A:ASP681 3.6 38.4 1.0
N A:PRO682 3.6 38.2 1.0
O A:ASP681 3.8 36.2 1.0
N A:ASP681 3.9 38.9 1.0
CD A:ARG686 4.0 57.1 1.0
CA A:ASP681 4.0 39.1 1.0
O A:HOH1105 4.0 45.5 1.0
CD A:PRO682 4.0 40.2 1.0
CA A:PRO682 4.1 37.4 1.0
CZ A:ARG686 4.2 74.0 1.0
C A:LYS680 4.4 41.4 1.0
CG A:PRO682 4.4 40.8 1.0
NE A:ARG686 4.5 71.4 1.0
O A:HOH1128 4.5 60.1 1.0
O A:HOH1161 4.6 57.8 1.0
O A:HOH1195 4.7 31.3 1.0
O A:LYS680 4.8 42.5 1.0
CB A:PRO682 4.9 38.4 1.0
CA A:LYS680 5.0 41.8 1.0

Iodine binding site 5 out of 7 in 5bvo

Go back to Iodine Binding Sites List in 5bvo
Iodine binding site 5 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:0.2
occ:1.00
 NE2 A:HIS902 3.3 36.2 1.0
CB A:ALA748 4.1 31.2 1.0
N A:GLN749 4.1 30.6 1.0
C A:ALA748 4.1 29.9 1.0
CG A:GLN749 4.2 33.0 1.0
O A:ALA748 4.2 29.7 1.0
CD2 A:HIS902 4.2 35.2 1.0
CA A:GLN749 4.3 30.6 1.0
CE1 A:HIS902 4.3 38.3 1.0
CB A:SER752 4.7 30.3 1.0
CA A:ALA748 4.8 31.1 1.0
CE1 A:HIS745 4.8 44.6 1.0
CB A:GLN749 4.8 32.1 1.0
ND1 A:HIS745 4.8 42.9 1.0

Iodine binding site 6 out of 7 in 5bvo

Go back to Iodine Binding Sites List in 5bvo
Iodine binding site 6 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:54.6
occ:1.00
 O A:PRO659 3.7 70.0 1.0
CA A:ASP660 4.2 68.2 1.0
C A:PRO659 4.2 66.7 1.0
CB A:ASP660 4.4 71.8 1.0
N A:ASP660 4.4 66.3 1.0

Iodine binding site 7 out of 7 in 5bvo

Go back to Iodine Binding Sites List in 5bvo
Iodine binding site 7 out of 7 in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1007

b:69.5
occ:1.00
 H51 A:4VE1008 3.5 31.5 0.9
CA A:GLY617 3.6 67.5 1.0
N A:GLU618 3.6 72.6 1.0
C A:GLY617 3.8 70.6 1.0
H50 A:4VE1008 3.9 31.8 0.9
CG2 A:VAL624 4.0 51.2 1.0
I A:IOD1003 4.0 0.8 1.0
N A:GLY617 4.1 61.6 1.0
CB A:VAL624 4.2 48.1 1.0
CE2 A:PHE785 4.3 40.1 1.0
C31 A:4VE1008 4.3 32.5 0.9
C A:GLU618 4.4 71.8 1.0
C30 A:4VE1008 4.5 31.4 0.9
CA A:GLU618 4.5 75.5 1.0
O A:LEU616 4.5 60.8 1.0
C A:LEU616 4.5 57.5 1.0
CD2 A:PHE785 4.6 36.8 1.0
O A:GLY617 4.7 71.8 1.0
O23 A:4VE1008 4.7 28.7 0.9

Reference:

C.W.Murray, V.Berdini, I.M.Buck, M.E.Carr, A.Cleasby, J.E.Coyle, J.E.Curry, J.E.Day, P.J.Day, K.Hearn, A.Iqbal, L.Y.Lee, V.Martins, P.N.Mortenson, J.M.Munck, L.W.Page, S.Patel, S.Roomans, K.Smith, E.Tamanini, G.Saxty. Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors. Acs Med.Chem.Lett. V. 6 798 2015.
ISSN: ISSN 1948-5875
PubMed: 26191369
DOI: 10.1021/ACSMEDCHEMLETT.5B00143
Page generated: Sun Aug 11 20:35:57 2024

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