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Iodine in PDB 5bvk: 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: 5bvk 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) 52.00 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.026, 71.505, 76.682, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.2

Other elements in 5bvk:

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

Iodine binding site 1 out of 6 in 5bvk

Go back to Iodine Binding Sites List in 5bvk
Iodine binding site 1 out of 6 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:31.9
occ:1.00
 CA A:PHE845 3.9 24.1 1.0
N A:GLN847 3.9 30.2 1.0
CB A:GLN847 3.9 36.4 1.0
C A:PHE845 4.0 25.8 1.0
N A:GLY846 4.2 24.2 1.0
CG A:LEU848 4.3 31.5 1.0
CA A:GLN847 4.3 32.1 1.0
O A:PHE845 4.5 29.5 1.0
CG A:GLN847 4.5 39.2 1.0
N A:LEU848 4.6 28.5 1.0
CD1 A:PHE845 4.7 25.3 1.0
C A:GLN847 4.7 30.9 1.0
N A:PHE845 4.8 22.3 1.0
CD1 A:LEU848 4.8 29.6 1.0
CB A:PHE845 4.8 24.3 1.0
C A:GLY846 4.9 28.1 1.0

Iodine binding site 2 out of 6 in 5bvk

Go back to Iodine Binding Sites List in 5bvk
Iodine binding site 2 out of 6 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:59.1
occ:0.75
 CD1 A:LEU883 3.1 32.9 1.0
NE A:ARG886 3.9 39.1 1.0
NH2 A:ARG886 4.0 39.3 1.0
CB A:PRO896 4.1 27.3 1.0
O A:GLN900 4.1 26.7 1.0
OE1 A:GLN900 4.2 44.9 1.0
CG A:PRO896 4.3 26.2 1.0
CB A:PHE904 4.3 28.5 1.0
C A:GLN900 4.4 27.9 1.0
CB A:GLN900 4.4 33.9 1.0
CG A:LEU883 4.4 27.6 1.0
CZ A:ARG886 4.5 41.7 1.0
CD1 A:PHE904 4.6 31.4 1.0
CG A:PHE904 4.6 29.1 1.0
CD2 A:LEU901 4.7 20.9 1.0
N A:LEU901 4.7 25.0 1.0
CA A:LEU901 4.8 23.1 1.0
CG A:GLN900 4.9 43.5 1.0
CD A:GLN900 5.0 50.1 1.0
CD A:ARG886 5.0 38.2 1.0

Iodine binding site 3 out of 6 in 5bvk

Go back to Iodine Binding Sites List in 5bvk
Iodine binding site 3 out of 6 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:64.0
occ:0.50
 N A:GLN620 3.0 45.9 1.0
N A:PHE621 3.2 45.3 1.0
N A:GLY622 3.3 42.6 1.0
NZ A:LYS655 3.3 24.6 1.0
CA A:GLY786 3.7 47.4 1.0
C A:GLY619 3.8 45.6 1.0
CA A:GLY619 3.8 41.7 1.0
CE A:LYS655 3.8 26.0 1.0
CD1 A:PHE621 3.8 50.3 1.0
CA A:GLN620 3.9 49.3 1.0
CE1 A:PHE621 3.9 53.4 1.0
CG A:PHE621 3.9 47.7 1.0
CA A:GLY622 4.0 35.9 1.0
C A:GLN620 4.0 46.8 1.0
CA A:PHE621 4.1 47.6 1.0
C A:PHE621 4.1 46.3 1.0
CZ A:PHE621 4.1 52.5 1.0
I A:IOD1006 4.1 52.2 0.8
CD2 A:PHE621 4.1 49.1 1.0
CE2 A:PHE621 4.1 49.1 1.0
CB A:GLN620 4.3 52.0 1.0
N A:GLY786 4.4 47.4 1.0
O A:GLY622 4.4 37.2 1.0
C A:GLY622 4.5 35.7 1.0
C A:GLY786 4.6 48.2 1.0
CB A:PHE621 4.6 47.2 1.0
N A:GLY619 4.8 44.9 1.0
O A:GLY619 4.9 49.4 1.0
N A:MET787 4.9 48.9 1.0

Iodine binding site 4 out of 6 in 5bvk

Go back to Iodine Binding Sites List in 5bvk
Iodine binding site 4 out of 6 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:51.5
occ:0.25
 NE2 A:HIS902 3.2 28.9 1.0
CD2 A:HIS902 4.0 26.6 1.0
N A:GLN749 4.0 22.1 1.0
CB A:ALA748 4.0 21.6 1.0
C A:ALA748 4.0 22.0 1.0
O A:HOH1130 4.1 34.9 1.0
O A:ALA748 4.1 22.8 1.0
CG A:GLN749 4.2 23.9 1.0
CA A:GLN749 4.2 22.0 1.0
CE1 A:HIS902 4.3 30.4 1.0
CB A:SER752 4.7 21.7 1.0
CA A:ALA748 4.7 21.2 1.0
CE1 A:HIS745 4.8 29.7 1.0
CB A:GLN749 4.8 22.8 1.0
ND1 A:HIS745 4.8 30.5 1.0

Iodine binding site 5 out of 6 in 5bvk

Go back to Iodine Binding Sites List in 5bvk
Iodine binding site 5 out of 6 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:70.3
occ:0.75
 O A:PRO659 3.8 40.3 1.0
CA A:ASP660 4.1 42.2 1.0
CB A:ASP660 4.6 45.1 1.0
C A:PRO659 4.7 38.8 1.0
C A:ASP660 4.8 41.0 1.0
N A:ASP660 4.8 39.5 1.0

Iodine binding site 6 out of 6 in 5bvk

Go back to Iodine Binding Sites List in 5bvk
Iodine binding site 6 out of 6 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:52.2
occ:0.75
 NZ A:LYS655 3.3 24.6 1.0
CE A:LYS655 3.6 26.0 1.0
N A:GLY786 3.6 47.4 1.0
N A:MET787 3.6 48.9 1.0
CE A:MET787 3.6 59.6 1.0
H26 A:4VC1007 3.8 43.2 1.0
CD A:LYS655 3.8 24.0 1.0
CG2 A:VAL624 4.0 28.1 1.0
I A:IOD1003 4.1 64.0 0.5
CA A:GLY786 4.1 47.4 1.0
CB A:MET787 4.1 54.2 1.0
CG A:MET787 4.2 55.9 1.0
C A:GLY786 4.4 48.2 1.0
CA A:GLY619 4.4 41.7 1.0
CA A:PHE785 4.5 48.8 1.0
C A:PHE785 4.5 47.1 1.0
CA A:MET787 4.5 51.9 1.0
CB A:PHE785 4.5 51.3 1.0
N A:GLY619 4.6 44.9 1.0
CD2 A:PHE785 4.6 52.0 1.0
H30 A:4VC1007 4.7 41.9 1.0
C12 A:4VC1007 4.7 44.3 1.0
SD A:MET787 4.8 61.6 1.0
CG A:LYS655 4.9 24.4 1.0
C A:GLY622 4.9 35.7 1.0
O A:GLY622 4.9 37.2 1.0
H25 A:4VC1007 5.0 43.0 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 Aug 11 20:35:57 2024

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