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Fluorine in PDB 6hp9: Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor

Enzymatic activity of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor

All present enzymatic activity of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor:
2.7.10.1;

Protein crystallography data

The structure of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor, PDB code: 6hp9 was solved by D.M.Pinkas, A.E.Fox, K.Kupinska, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.N.Bullock, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.08 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.510, 65.890, 162.880, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor (pdb code 6hp9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor, PDB code: 6hp9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hp9

Go back to Fluorine Binding Sites List in 6hp9
Fluorine binding site 1 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:28.5
occ:1.00
 F A:GKB1001 0.0 28.5 1.0
C4 A:GKB1001 1.3 34.4 1.0
F2 A:GKB1001 2.1 30.6 1.0
F1 A:GKB1001 2.1 33.5 1.0
C3 A:GKB1001 2.4 30.3 1.0
C5 A:GKB1001 2.7 28.1 1.0
CD1 A:LEU679 3.3 35.4 1.0
CE2 A:PHE762 3.5 31.0 1.0
C2 A:GKB1001 3.6 28.8 1.0
CZ A:PHE762 3.7 43.3 1.0
O A:HOH1187 4.1 29.0 1.0
C6 A:GKB1001 4.1 32.9 1.0
CD2 A:HIS764 4.2 28.4 1.0
CD2 A:PHE762 4.5 30.4 1.0
NE2 A:HIS764 4.6 30.8 1.0
CD1 A:LEU757 4.7 33.4 1.0
CD2 A:LEU757 4.7 28.8 1.0
C1 A:GKB1001 4.8 28.6 1.0
CG A:LEU679 4.8 34.2 1.0
CG2 A:ILE684 4.8 27.4 1.0
CE1 A:PHE762 4.9 48.0 1.0
C11 A:GKB1001 5.0 29.8 1.0

Fluorine binding site 2 out of 6 in 6hp9

Go back to Fluorine Binding Sites List in 6hp9
Fluorine binding site 2 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:33.5
occ:1.00
 F1 A:GKB1001 0.0 33.5 1.0
C4 A:GKB1001 1.3 34.4 1.0
F2 A:GKB1001 2.1 30.6 1.0
F A:GKB1001 2.1 28.5 1.0
C3 A:GKB1001 2.4 30.3 1.0
C2 A:GKB1001 2.8 28.8 1.0
CD1 A:LEU679 3.3 35.4 1.0
CG2 A:ILE684 3.5 27.4 1.0
C5 A:GKB1001 3.5 28.1 1.0
CG2 A:ILE685 3.6 26.0 1.0
O A:ILE782 4.0 25.0 1.0
C1 A:GKB1001 4.2 28.6 1.0
CA A:ALA783 4.2 20.7 1.0
C A:ALA783 4.5 30.4 1.0
C A:ILE782 4.6 25.1 1.0
O A:HOH1191 4.6 32.5 1.0
C6 A:GKB1001 4.7 32.9 1.0
O A:GKB1001 4.7 31.6 1.0
N A:ALA783 4.7 26.8 1.0
CG A:LEU679 4.7 34.2 1.0
N A:ASP784 4.8 27.9 1.0
C11 A:GKB1001 4.9 29.8 1.0
N A:ILE685 4.9 29.6 1.0
O A:ALA783 4.9 26.0 1.0
CB A:ILE684 5.0 28.0 1.0

Fluorine binding site 3 out of 6 in 6hp9

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Fluorine binding site 3 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:30.6
occ:1.00
 F2 A:GKB1001 0.0 30.6 1.0
C4 A:GKB1001 1.3 34.4 1.0
F A:GKB1001 2.1 28.5 1.0
F1 A:GKB1001 2.1 33.5 1.0
C3 A:GKB1001 2.4 30.3 1.0
C2 A:GKB1001 3.1 28.8 1.0
C A:ALA783 3.2 30.4 1.0
O A:ALA783 3.2 26.0 1.0
NE2 A:HIS764 3.2 30.8 1.0
C5 A:GKB1001 3.3 28.1 1.0
CD2 A:HIS764 3.4 28.4 1.0
CA A:ALA783 3.6 20.7 1.0
N A:ASP784 3.7 27.9 1.0
CB A:ASP784 3.7 31.0 1.0
N A:ALA783 3.9 26.8 1.0
CG2 A:ILE782 4.2 29.4 1.0
CA A:ASP784 4.3 32.6 1.0
O A:ILE782 4.3 25.0 1.0
C A:ILE782 4.3 25.1 1.0
O A:HOH1187 4.3 29.0 1.0
CE1 A:HIS764 4.4 30.8 1.0
C1 A:GKB1001 4.4 28.6 1.0
C6 A:GKB1001 4.5 32.9 1.0
CG A:HIS764 4.6 32.4 1.0
O A:GKB1001 4.8 31.6 1.0
CG2 A:ILE685 4.9 26.0 1.0
CD1 A:LEU679 5.0 35.4 1.0
CB A:ALA783 5.0 22.1 1.0
CG A:ASP784 5.0 33.4 1.0
C11 A:GKB1001 5.0 29.8 1.0

Fluorine binding site 4 out of 6 in 6hp9

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Fluorine binding site 4 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:31.5
occ:1.00
 F B:GKB1001 0.0 31.5 1.0
C4 B:GKB1001 1.3 30.0 1.0
F2 B:GKB1001 2.1 30.4 1.0
F1 B:GKB1001 2.1 31.6 1.0
C3 B:GKB1001 2.4 27.4 1.0
C5 B:GKB1001 2.7 25.4 1.0
CD1 B:LEU679 3.5 32.2 1.0
C2 B:GKB1001 3.6 26.1 1.0
CE2 B:PHE762 3.6 34.2 1.0
O B:HOH1152 4.1 26.6 1.0
C6 B:GKB1001 4.1 31.9 1.0
CD2 B:HIS764 4.2 29.3 1.0
CZ B:PHE762 4.2 32.9 1.0
CD1 B:LEU757 4.4 26.3 1.0
CD2 B:PHE762 4.4 31.0 1.0
CD2 B:LEU757 4.5 28.5 1.0
NE2 B:HIS764 4.6 28.8 1.0
CG2 B:ILE684 4.7 29.4 1.0
C1 B:GKB1001 4.8 24.6 1.0
CG B:LEU679 4.9 30.9 1.0
C11 B:GKB1001 5.0 26.2 1.0
N1 B:GKB1001 5.0 29.9 1.0

Fluorine binding site 5 out of 6 in 6hp9

Go back to Fluorine Binding Sites List in 6hp9
Fluorine binding site 5 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:31.6
occ:1.00
 F1 B:GKB1001 0.0 31.6 1.0
C4 B:GKB1001 1.3 30.0 1.0
F2 B:GKB1001 2.1 30.4 1.0
F B:GKB1001 2.1 31.5 1.0
C3 B:GKB1001 2.4 27.4 1.0
C2 B:GKB1001 2.9 26.1 1.0
CG2 B:ILE684 3.4 29.4 1.0
C5 B:GKB1001 3.5 25.4 1.0
CD1 B:LEU679 3.5 32.2 1.0
CG2 B:ILE685 3.8 33.5 1.0
O B:ILE782 3.8 29.8 1.0
C1 B:GKB1001 4.2 24.6 1.0
CA B:ALA783 4.3 24.4 1.0
C B:ILE782 4.6 29.8 1.0
C B:ALA783 4.6 26.9 1.0
C6 B:GKB1001 4.7 31.9 1.0
N B:ILE685 4.8 28.6 1.0
O B:ILE685 4.8 32.8 1.0
O B:GKB1001 4.8 26.1 1.0
N B:ALA783 4.8 26.4 1.0
CG B:LEU679 4.8 30.9 1.0
CB B:ILE684 4.8 29.1 1.0
C11 B:GKB1001 4.9 26.2 1.0
CB B:LEU679 5.0 34.4 1.0
O B:ALA783 5.0 26.3 1.0

Fluorine binding site 6 out of 6 in 6hp9

Go back to Fluorine Binding Sites List in 6hp9
Fluorine binding site 6 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Kinase Domain of Human DDR1 in Complex with A 2- Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:30.4
occ:1.00
 F2 B:GKB1001 0.0 30.4 1.0
C4 B:GKB1001 1.3 30.0 1.0
F B:GKB1001 2.1 31.5 1.0
F1 B:GKB1001 2.1 31.6 1.0
C3 B:GKB1001 2.4 27.4 1.0
C2 B:GKB1001 3.0 26.1 1.0
O B:ALA783 3.1 26.3 1.0
C B:ALA783 3.1 26.9 1.0
C5 B:GKB1001 3.3 25.4 1.0
CA B:ALA783 3.4 24.4 1.0
NE2 B:HIS764 3.5 28.8 1.0
CD2 B:HIS764 3.6 29.3 1.0
N B:ASP784 3.7 29.8 1.0
CB B:ASP784 3.8 29.7 1.0
N B:ALA783 3.8 26.4 1.0
O B:ILE782 3.9 29.8 1.0
C B:ILE782 4.1 29.8 1.0
CG2 B:ILE782 4.1 28.4 1.0
CA B:ASP784 4.3 26.8 1.0
C1 B:GKB1001 4.3 24.6 1.0
O B:HOH1152 4.5 26.6 1.0
C6 B:GKB1001 4.5 31.9 1.0
CE1 B:HIS764 4.6 27.6 1.0
O B:GKB1001 4.7 26.1 1.0
CB B:ALA783 4.8 26.9 1.0
CG B:HIS764 4.8 28.6 1.0
CG2 B:ILE685 4.9 33.5 1.0
CB B:ILE782 4.9 33.4 1.0
C11 B:GKB1001 4.9 26.2 1.0
CG2 B:ILE684 5.0 29.4 1.0

Reference:

D.Zhu, H.Huang, D.M.Pinkas, J.Luo, D.Ganguly, A.E.Fox, E.Arner, Q.Xiang, Z.C.Tu, A.N.Bullock, R.A.Brekken, K.Ding, X.Lu. 2-Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-Based Discoidin Domain Receptor 1 (DDR1) Inhibitors: Design, Synthesis, and in Vivo Antipancreatic Cancer Efficacy. J.Med.Chem. V. 62 7431 2019.
ISSN: ISSN 0022-2623
PubMed: 31310125
DOI: 10.1021/ACS.JMEDCHEM.9B00365
Page generated: Thu Aug 1 21:17:46 2024

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