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Iodine in PDB 5bvw: 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: 5bvw 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) 32.80 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.642, 72.780, 75.787, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.4

Other elements in 5bvw:

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

Chlorine (Cl) 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 5bvw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors, PDB code: 5bvw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 5bvw

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Iodine binding site 1 out of 8 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:35.8
occ:1.00
O A:HOH1261 3.6 16.9 0.5
CA A:PHE845 3.8 28.4 1.0
N A:GLN847 3.9 32.9 1.0
C A:PHE845 3.9 32.5 1.0
CB A:GLN847 4.1 36.2 1.0
N A:GLY846 4.2 31.5 1.0
CG A:LEU848 4.2 34.2 1.0
O A:PHE845 4.3 32.7 1.0
CA A:GLN847 4.4 34.1 1.0
N A:LEU848 4.6 33.5 1.0
CG A:GLN847 4.6 43.7 1.0
C A:GLN847 4.7 38.5 1.0
CD2 A:LEU848 4.7 31.2 1.0
O A:HOH1172 4.7 39.0 1.0
N A:PHE845 4.7 27.3 1.0
CB A:PHE845 4.8 29.3 1.0
CD1 A:PHE845 4.9 31.5 1.0
CD1 A:LEU848 4.9 32.8 1.0
C A:GLY846 5.0 36.9 1.0

Iodine binding site 2 out of 8 in 5bvw

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Iodine binding site 2 out of 8 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:54.8
occ:1.00
CD1 A:LEU883 2.8 41.7 1.0
NH2 A:ARG886 3.6 47.8 1.0
NE A:ARG886 3.8 46.7 1.0
CG A:PRO896 4.0 37.1 1.0
CB A:PRO896 4.0 34.2 1.0
CG A:LEU883 4.2 37.4 1.0
CZ A:ARG886 4.2 55.8 1.0
O A:GLN900 4.3 39.0 1.0
CB A:PHE904 4.3 31.6 1.0
CD2 A:LEU901 4.4 33.7 1.0
CD2 A:LEU883 4.4 39.2 1.0
C A:GLN900 4.4 38.2 1.0
CD1 A:PHE904 4.4 33.3 1.0
CB A:GLN900 4.4 34.3 1.0
N A:LEU901 4.6 32.5 1.0
CA A:LEU901 4.6 30.8 1.0
CG A:PHE904 4.6 32.0 1.0
OE1 A:GLN900 4.7 53.7 1.0
CB A:LEU883 4.8 32.2 1.0
CG A:GLN900 4.9 53.5 1.0
CD A:ARG886 4.9 41.5 1.0

Iodine binding site 3 out of 8 in 5bvw

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Iodine binding site 3 out of 8 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:51.1
occ:0.50
O A:HOH1291 3.1 64.0 1.0
CE A:LYS655 3.3 45.9 1.0
NZ A:LYS655 3.3 44.0 1.0
I A:IOD1008 3.3 89.2 1.0
N A:GLY622 3.5 48.1 1.0
N A:GLN620 3.6 55.3 1.0
CA A:GLY619 3.7 50.5 1.0
N A:PHE621 3.8 53.5 1.0
C A:GLY619 3.8 56.4 1.0
CA A:GLY622 3.9 45.0 1.0
O A:GLY622 4.0 42.5 1.0
N A:GLY619 4.1 48.6 1.0
C A:GLY622 4.2 44.6 1.0
CE2 A:PHE621 4.2 57.8 1.0
C A:PHE621 4.2 54.7 1.0
CD2 A:PHE621 4.3 55.4 1.0
CZ A:PHE621 4.4 56.4 1.0
CG A:PHE621 4.4 54.3 1.0
CE1 A:PHE621 4.5 57.9 1.0
CD1 A:PHE621 4.5 57.0 1.0
CA A:PHE621 4.5 53.0 1.0
CA A:GLN620 4.6 56.8 1.0
C A:GLN620 4.7 59.6 1.0
O A:GLY619 4.7 56.0 1.0
CD A:LYS655 4.7 38.6 1.0
O A:HOH1285 4.8 53.3 1.0
O A:HOH1183 5.0 42.4 1.0

Iodine binding site 4 out of 8 in 5bvw

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Iodine binding site 4 out of 8 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:64.9
occ:0.50
O A:HOH1358 3.2 65.8 1.0
NH1 A:ARG686 3.4 72.8 1.0
C A:ASP681 3.5 38.0 1.0
O A:HOH1203 3.5 38.2 1.0
O A:ASP681 3.6 39.2 1.0
N A:PRO682 3.7 35.0 1.0
CA A:PRO682 3.9 34.5 1.0
N A:ASP681 4.0 33.6 1.0
CD A:ARG686 4.1 57.1 1.0
CA A:ASP681 4.1 33.9 1.0
CD A:PRO682 4.3 38.2 1.0
CZ A:ARG686 4.4 87.5 1.0
CG A:PRO682 4.5 43.7 1.0
O A:HOH1297 4.6 79.7 1.0
C A:LYS680 4.6 37.4 1.0
NE A:ARG686 4.7 75.6 1.0
O A:HOH1215 4.7 36.0 1.0
CB A:PRO682 4.8 37.9 1.0
O A:HOH1136 4.9 65.0 1.0

Iodine binding site 5 out of 8 in 5bvw

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Iodine binding site 5 out of 8 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:47.1
occ:0.50
NE2 A:HIS902 3.3 33.8 1.0
O A:HOH1265 3.9 46.1 1.0
C A:ALA748 4.0 31.0 1.0
O A:ALA748 4.1 30.4 1.0
N A:GLN749 4.1 29.5 1.0
CB A:ALA748 4.1 26.8 1.0
CG A:GLN749 4.1 30.2 1.0
CD2 A:HIS902 4.2 33.1 1.0
CA A:GLN749 4.2 29.1 1.0
CE1 A:HIS902 4.4 34.8 1.0
O A:HOH1262 4.5 64.2 1.0
CB A:SER752 4.5 31.5 1.0
CA A:ALA748 4.7 26.9 1.0
CB A:GLN749 4.8 29.5 1.0
ND1 A:HIS745 4.8 39.1 1.0
CE1 A:HIS745 4.8 38.9 1.0
O A:HOH1364 4.9 67.9 1.0

Iodine binding site 6 out of 8 in 5bvw

Go back to Iodine Binding Sites List in 5bvw
Iodine binding site 6 out of 8 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:53.6
occ:0.50
O A:PRO659 3.4 43.3 1.0
CA A:ASP660 4.1 43.1 1.0
C A:PRO659 4.4 41.5 1.0
C A:ASP660 4.7 47.1 1.0
N A:ASP660 4.8 40.0 1.0
CB A:ASP660 4.9 46.8 1.0
O A:ASP660 4.9 47.2 1.0

Iodine binding site 7 out of 8 in 5bvw

Go back to Iodine Binding Sites List in 5bvw
Iodine binding site 7 out of 8 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:54.0
occ:1.00
N A:LEU718 3.4 35.0 1.0
CA A:GLN717 3.8 38.3 1.0
CG A:GLN717 4.1 57.7 1.0
C A:GLN717 4.1 39.5 1.0
CB A:GLN717 4.2 41.2 1.0
CD2 A:LEU839 4.3 39.0 1.0
CB A:LEU718 4.3 33.3 1.0
NH2 A:ARG841 4.3 44.1 1.0
CZ A:ARG841 4.5 62.3 1.0
CA A:LEU718 4.5 33.7 1.0
CD1 A:LEU839 4.6 34.3 1.0
CG A:LEU839 4.8 33.7 1.0
CB A:LEU839 4.8 29.3 1.0
NH1 A:ARG841 4.8 36.5 1.0
O A:HIS716 4.8 40.1 1.0
NE A:ARG841 4.8 50.4 1.0
O A:HOH1158 4.9 38.4 1.0
CD A:GLN717 5.0 75.2 1.0

Iodine binding site 8 out of 8 in 5bvw

Go back to Iodine Binding Sites List in 5bvw
Iodine binding site 8 out of 8 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 8 of Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1008

b:89.2
occ:1.00
I A:IOD1003 3.3 51.1 0.5
N A:GLY619 3.5 48.6 1.0
CE A:LYS655 3.9 45.9 1.0
C A:GLU618 3.9 50.0 1.0
CG2 A:VAL624 3.9 34.2 1.0
CA A:GLY619 3.9 50.5 1.0
O A:GLY622 4.0 42.5 1.0
NZ A:LYS655 4.0 44.0 1.0
O A:HOH1324 4.3 67.4 1.0
CA A:GLU618 4.3 47.3 1.0
C A:GLY622 4.3 44.6 1.0
C A:GLY786 4.3 0.7 1.0
O A:GLY786 4.3 79.1 1.0
N A:GLU618 4.4 46.5 1.0
O A:HOH1183 4.5 42.4 1.0
CD A:LYS655 4.5 38.6 1.0
O A:GLU618 4.5 47.1 1.0
N A:GLU623 4.6 37.8 1.0
O A:HOH1291 4.7 64.0 1.0
N A:VAL624 4.7 34.0 1.0
N A:GLY786 4.8 69.0 1.0
CG A:LYS655 4.8 39.7 1.0
CA A:GLU623 4.9 36.3 1.0
C A:GLY617 4.9 48.0 1.0
CA A:GLY622 5.0 45.0 1.0

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 Dec 13 19:38:32 2020

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