Atomistry » Iodine » PDB 5b34-5ems » 5bvk
Atomistry »
  Iodine »
    PDB 5b34-5ems »
      5bvk »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy