Fluorine in PDB 6gpx: Crystal Structure of CCR2A in Complex with Mk-0812

The structure of Crystal Structure of CCR2A in Complex with Mk-0812, PDB code: 6gpx was solved by A.Pautsch, G.Schnapp, R.Cheng, A.Apel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.570, 64.550, 131.200, 90.00, 91.19, 90.00
R / Rfree (%)	23 / 24.3

The structure of Crystal Structure of CCR2A in Complex with Mk-0812 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of CCR2A in Complex with Mk-0812 (pdb code 6gpx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of CCR2A in Complex with Mk-0812, PDB code: 6gpx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of CCR2A in Complex with Mk-0812


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of CCR2A in Complex with Mk-0812 within 5.0Å range: probe atom residue distance (Å) B Occ A:F413 b:50.6 occ:1.00 F30 A:F7N413 0.0 50.6 1.0 C29 A:F7N413 1.3 49.9 1.0 F32 A:F7N413 2.1 50.3 1.0 F31 A:F7N413 2.1 50.8 1.0 C17 A:F7N413 2.4 47.7 1.0 H52 A:F7N413 2.5 45.9 0.0 HA A:VAL340 2.6 40.3 0.0 HG22 A:VAL340 2.8 43.3 0.0 C18 A:F7N413 2.8 45.9 1.0 H9 A:OLA407 2.9 89.5 0.0 H62 A:OLA407 2.9 92.7 0.0 HD11 A:LEU45 3.5 62.0 0.0 HG23 A:VAL340 3.6 43.3 0.0 CG2 A:VAL340 3.6 43.3 1.0 C16 A:F7N413 3.6 47.0 1.0 CA A:VAL340 3.6 40.3 1.0 HB A:THR343 3.8 46.2 0.0 C9 A:OLA407 3.9 89.5 1.0 O A:GLN339 3.9 45.7 1.0 N A:VAL340 4.0 40.9 1.0 H51 A:F7N413 4.0 47.0 0.0 H42 A:OLA407 4.0 96.0 0.0 OG1 A:THR343 4.0 44.8 1.0 C6 A:OLA407 4.0 92.7 1.0 C A:GLN339 4.1 45.7 1.0 HD23 A:LEU44 4.1 67.4 0.0 HB3 A:GLN339 4.1 43.9 0.0 CB A:VAL340 4.1 43.8 1.0 C13 A:F7N413 4.2 44.9 1.0 HG13 A:VAL340 4.2 43.6 0.0 H61 A:OLA407 4.4 92.8 0.0 H10 A:OLA407 4.4 88.8 0.0 CB A:THR343 4.5 46.2 1.0 HG22 A:ILE40 4.5 75.5 0.0 CD1 A:LEU45 4.5 62.0 1.0 HG21 A:THR343 4.5 41.7 0.0 HG21 A:VAL340 4.5 43.4 0.0 HG22 A:VAL37 4.5 88.2 0.0 HG23 A:VAL37 4.5 88.2 0.0 H A:VAL340 4.6 40.9 0.0 HD13 A:LEU45 4.6 62.0 0.0 C10 A:OLA407 4.6 88.8 1.0 HA2 A:GLY41 4.6 68.5 0.0 C8 A:OLA407 4.7 90.2 1.0 H82 A:OLA407 4.7 90.3 0.0 C A:VAL340 4.7 43.8 1.0 N15 A:F7N413 4.7 46.6 1.0 O A:VAL340 4.7 43.9 1.0 H41 A:OLA407 4.7 96.0 0.0 CG1 A:VAL340 4.8 43.6 1.0 C4 A:OLA407 4.8 96.0 1.0 HG1 A:THR343 4.8 44.8 0.0 C5 A:OLA407 4.8 94.4 1.0 C7 A:OLA407 4.8 91.3 1.0 HD12 A:LEU45 4.8 62.0 0.0 HB2 A:GLN339 4.8 43.8 0.0 CB A:GLN339 4.9 43.8 1.0 HD21 A:LEU45 4.9 64.0 0.0 C14 A:F7N413 4.9 45.5 1.0 H51 A:OLA407 4.9 94.4 0.0 H49 A:F7N413 5.0 44.0 0.0 CG2 A:VAL37 5.0 88.2 1.0 H A:THR343 5.0 40.7 0.0

Fluorine binding site 2 out of 6 in the Crystal Structure of CCR2A in Complex with Mk-0812


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of CCR2A in Complex with Mk-0812 within 5.0Å range: probe atom residue distance (Å) B Occ A:F413 b:50.8 occ:1.00 F31 A:F7N413 0.0 50.8 1.0 C29 A:F7N413 1.3 49.9 1.0 F32 A:F7N413 2.1 50.3 1.0 F30 A:F7N413 2.1 50.6 1.0 C17 A:F7N413 2.3 47.7 1.0 HD11 A:LEU45 2.6 62.0 0.0 HA2 A:GLY41 2.6 68.5 0.0 HD13 A:LEU45 2.9 62.0 0.0 HG22 A:ILE40 3.0 75.5 0.0 HD23 A:LEU44 3.1 67.4 0.0 C16 A:F7N413 3.2 47.0 1.0 CD1 A:LEU45 3.2 62.0 1.0 C18 A:F7N413 3.2 45.9 1.0 H51 A:F7N413 3.3 47.0 0.0 H52 A:F7N413 3.3 45.9 0.0 CA A:GLY41 3.5 68.5 1.0 HD12 A:LEU45 3.7 62.0 0.0 HB3 A:LEU44 3.7 59.7 0.0 H62 A:OLA407 3.7 92.7 0.0 N A:GLY41 3.7 69.4 1.0 HA3 A:GLY41 3.8 68.5 0.0 H A:GLY41 4.1 69.4 0.0 CD2 A:LEU44 4.1 67.4 1.0 C A:ILE40 4.1 74.4 1.0 CG2 A:ILE40 4.1 75.5 1.0 H9 A:OLA407 4.2 89.5 0.0 O A:ILE40 4.2 74.3 1.0 HD22 A:LEU45 4.2 63.9 0.0 HB A:ILE40 4.2 75.1 0.0 HD22 A:LEU44 4.3 67.5 0.0 N15 A:F7N413 4.4 46.6 1.0 H61 A:OLA407 4.4 92.8 0.0 HD21 A:LEU45 4.4 64.0 0.0 C13 A:F7N413 4.5 44.9 1.0 CG A:LEU45 4.5 61.9 1.0 HG21 A:ILE40 4.5 75.5 0.0 HG22 A:VAL340 4.5 43.3 0.0 O A:VAL37 4.6 84.2 1.0 C6 A:OLA407 4.6 92.7 1.0 CD2 A:LEU45 4.6 63.9 1.0 OG1 A:THR343 4.6 44.8 1.0 HG21 A:THR343 4.7 41.7 0.0 CB A:ILE40 4.7 75.1 1.0 CB A:LEU44 4.7 59.8 1.0 HG22 A:VAL37 4.7 88.2 0.0 HD21 A:LEU44 4.7 67.5 0.0 HA A:VAL340 4.7 40.3 0.0 HG23 A:ILE40 4.7 75.5 0.0 C A:GLY41 4.8 70.3 1.0 H82 A:OLA407 4.8 90.3 0.0 H42 A:OLA407 4.8 96.0 0.0 H41 A:OLA407 4.8 96.0 0.0 C9 A:OLA407 4.8 89.5 1.0 CG A:LEU44 4.9 65.0 1.0 C14 A:F7N413 4.9 45.5 1.0 H A:LEU45 4.9 57.8 0.0 O A:GLY41 5.0 70.0 1.0 HG23 A:VAL37 5.0 88.2 0.0

Fluorine binding site 3 out of 6 in the Crystal Structure of CCR2A in Complex with Mk-0812


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of CCR2A in Complex with Mk-0812 within 5.0Å range: probe atom residue distance (Å) B Occ A:F413 b:50.3 occ:1.00 F32 A:F7N413 0.0 50.3 1.0 C29 A:F7N413 1.3 49.9 1.0 F30 A:F7N413 2.1 50.6 1.0 F31 A:F7N413 2.1 50.8 1.0 C17 A:F7N413 2.4 47.7 1.0 H51 A:F7N413 2.6 47.0 0.0 C16 A:F7N413 2.8 47.0 1.0 HG22 A:VAL37 2.9 88.2 0.0 HG23 A:VAL37 2.9 88.2 0.0 H42 A:OLA407 3.2 96.0 0.0 H62 A:OLA407 3.3 92.7 0.0 CG2 A:VAL37 3.4 88.2 1.0 HG22 A:VAL340 3.4 43.3 0.0 HG22 A:ILE40 3.5 75.5 0.0 O A:VAL37 3.5 84.2 1.0 C18 A:F7N413 3.6 45.9 1.0 H41 A:OLA407 3.6 96.0 0.0 HB A:ILE40 3.6 75.1 0.0 HG23 A:VAL340 3.8 43.3 0.0 C4 A:OLA407 3.9 96.0 1.0 H52 A:F7N413 3.9 45.9 0.0 HG21 A:VAL37 3.9 88.2 0.0 HA2 A:GLY41 4.0 68.5 0.0 HA A:VAL37 4.0 84.1 0.0 H A:GLY41 4.1 69.4 0.0 CG2 A:VAL340 4.1 43.3 1.0 N15 A:F7N413 4.1 46.6 1.0 C6 A:OLA407 4.2 92.7 1.0 N A:GLY41 4.2 69.4 1.0 H61 A:OLA407 4.2 92.8 0.0 CG2 A:ILE40 4.2 75.5 1.0 HB3 A:GLN339 4.3 43.9 0.0 HG21 A:ILE40 4.3 75.5 0.0 HA A:VAL340 4.3 40.3 0.0 CB A:ILE40 4.4 75.1 1.0 C A:VAL37 4.4 84.9 1.0 HA3 A:GLY41 4.4 68.5 0.0 CA A:GLY41 4.5 68.5 1.0 H9 A:OLA407 4.5 89.5 0.0 HD11 A:LEU45 4.5 62.0 0.0 H21 A:OLA407 4.5 99.5 0.0 C5 A:OLA407 4.6 94.4 1.0 CB A:VAL37 4.6 88.3 1.0 CA A:VAL37 4.6 84.0 1.0 C13 A:F7N413 4.7 44.9 1.0 C A:ILE40 4.7 74.4 1.0 HG21 A:VAL340 4.8 43.4 0.0 HB2 A:GLN339 4.8 43.8 0.0 HD23 A:LEU44 4.8 67.4 0.0 C14 A:F7N413 4.9 45.5 1.0 HD13 A:LEU45 4.9 62.0 0.0 H51 A:OLA407 5.0 94.4 0.0

Fluorine binding site 4 out of 6 in the Crystal Structure of CCR2A in Complex with Mk-0812


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of CCR2A in Complex with Mk-0812 within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:57.5 occ:1.00 F30 B:F7N404 0.0 57.5 1.0 C29 B:F7N404 1.3 56.8 1.0 F32 B:F7N404 2.1 57.0 1.0 F31 B:F7N404 2.1 57.6 1.0 C17 B:F7N404 2.4 54.2 1.0 H52 B:F7N404 2.4 53.4 0.0 C18 B:F7N404 2.8 53.4 1.0 HA B:VAL289 2.9 55.9 0.0 HD11 B:LEU45 3.1 68.0 0.0 HG22 B:VAL289 3.2 58.6 0.0 HD23 B:LEU44 3.5 75.3 0.0 HB B:THR292 3.5 60.5 0.0 C16 B:F7N404 3.7 53.1 1.0 OG1 B:THR292 3.7 61.8 1.0 HG21 B:THR292 3.9 58.9 0.0 CA B:VAL289 4.0 55.9 1.0 CD1 B:LEU45 4.0 68.0 1.0 H51 B:F7N404 4.1 53.1 0.0 CB B:THR292 4.1 60.5 1.0 CG2 B:VAL289 4.1 58.6 1.0 C13 B:F7N404 4.1 53.8 1.0 O B:GLN288 4.2 60.5 1.0 HD13 B:LEU45 4.2 68.0 0.0 HG23 B:VAL289 4.2 58.6 0.0 HD12 B:LEU45 4.3 68.0 0.0 HG22 B:ILE40 4.3 81.8 0.0 HG13 B:VAL289 4.3 59.1 0.0 CD2 B:LEU44 4.4 75.3 1.0 HG1 B:THR292 4.4 61.8 0.0 N B:VAL289 4.5 57.0 1.0 HA2 B:GLY41 4.5 72.1 0.0 C B:GLN288 4.5 60.9 1.0 CG2 B:THR292 4.5 58.9 1.0 CB B:VAL289 4.6 59.3 1.0 HG22 B:VAL37 4.6 0.3 0.0 HB3 B:GLN288 4.7 58.7 0.0 HD21 B:LEU44 4.7 75.3 0.0 HD22 B:LEU44 4.7 75.3 0.0 HD21 B:LEU45 4.7 69.2 0.0 O B:VAL289 4.8 57.8 1.0 N15 B:F7N404 4.8 53.6 1.0 H49 B:F7N404 4.9 53.3 0.0 C B:VAL289 4.9 58.4 1.0 C14 B:F7N404 5.0 53.8 1.0 H B:THR292 5.0 53.1 0.0 HG22 B:THR292 5.0 58.9 0.0 CG1 B:VAL289 5.0 59.1 1.0 HG23 B:VAL37 5.0 0.3 0.0 HG21 B:VAL289 5.0 58.6 0.0

Fluorine binding site 5 out of 6 in the Crystal Structure of CCR2A in Complex with Mk-0812


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of CCR2A in Complex with Mk-0812 within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:57.6 occ:1.00 F31 B:F7N404 0.0 57.6 1.0 C29 B:F7N404 1.3 56.8 1.0 F32 B:F7N404 2.1 57.0 1.0 F30 B:F7N404 2.1 57.5 1.0 C17 B:F7N404 2.4 54.2 1.0 HG22 B:ILE40 2.6 81.8 0.0 HA2 B:GLY41 2.7 72.1 0.0 H51 B:F7N404 2.9 53.1 0.0 C16 B:F7N404 3.0 53.1 1.0 HD11 B:LEU45 3.0 68.0 0.0 HD23 B:LEU44 3.1 75.3 0.0 HD13 B:LEU45 3.1 68.0 0.0 C18 B:F7N404 3.4 53.4 1.0 CA B:GLY41 3.5 72.1 1.0 CD1 B:LEU45 3.5 68.0 1.0 N B:GLY41 3.5 73.3 1.0 HB3 B:LEU44 3.6 67.7 0.0 CG2 B:ILE40 3.7 81.8 1.0 H52 B:F7N404 3.7 53.4 0.0 C B:ILE40 3.8 78.7 1.0 HA3 B:GLY41 3.8 72.1 0.0 HB B:ILE40 3.8 80.9 0.0 H B:GLY41 3.9 73.3 0.0 HD12 B:LEU45 4.0 68.0 0.0 O B:ILE40 4.0 78.0 1.0 CD2 B:LEU44 4.0 75.3 1.0 HG21 B:ILE40 4.1 81.8 0.0 HD22 B:LEU44 4.1 75.3 0.0 HG22 B:VAL37 4.1 0.3 0.0 N15 B:F7N404 4.3 53.6 1.0 CB B:ILE40 4.3 80.9 1.0 HG23 B:ILE40 4.4 81.8 0.0 O B:VAL37 4.4 99.2 1.0 HD22 B:LEU45 4.5 69.2 0.0 HG22 B:VAL289 4.6 58.6 0.0 CB B:LEU44 4.6 67.7 1.0 HG23 B:VAL37 4.6 0.3 0.0 C13 B:F7N404 4.6 53.8 1.0 CA B:ILE40 4.7 78.1 1.0 HD21 B:LEU44 4.7 75.3 0.0 C B:GLY41 4.8 73.8 1.0 HD21 B:LEU45 4.8 69.2 0.0 CG B:LEU45 4.8 67.7 1.0 HB2 B:LEU44 4.8 67.7 0.0 CG B:LEU44 4.9 73.1 1.0 CG2 B:VAL37 4.9 0.3 1.0 C14 B:F7N404 4.9 53.8 1.0 HA B:VAL289 5.0 55.9 0.0 HG21 B:THR292 5.0 58.9 0.0 CD2 B:LEU45 5.0 69.2 1.0 H B:LEU45 5.0 64.5 0.0

Fluorine binding site 6 out of 6 in the Crystal Structure of CCR2A in Complex with Mk-0812


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of CCR2A in Complex with Mk-0812 within 5.0Å range: probe atom residue distance (Å) B Occ B:F404 b:57.0 occ:1.00 F32 B:F7N404 0.0 57.0 1.0 C29 B:F7N404 1.3 56.8 1.0 F30 B:F7N404 2.1 57.5 1.0 F31 B:F7N404 2.1 57.6 1.0 C17 B:F7N404 2.4 54.2 1.0 HG22 B:VAL37 2.7 0.3 0.0 HG23 B:VAL37 2.9 0.3 0.0 HG22 B:VAL289 2.9 58.6 0.0 H51 B:F7N404 2.9 53.1 0.0 C16 B:F7N404 3.0 53.1 1.0 CG2 B:VAL37 3.2 0.3 1.0 HG23 B:VAL289 3.4 58.6 0.0 C18 B:F7N404 3.4 53.4 1.0 HG21 B:VAL37 3.5 0.3 0.0 CG2 B:VAL289 3.6 58.6 1.0 HG22 B:ILE40 3.7 81.8 0.0 H52 B:F7N404 3.7 53.4 0.0 HA B:VAL289 3.8 55.9 0.0 HB B:ILE40 4.0 80.9 0.0 O B:VAL37 4.2 99.2 1.0 HB3 B:GLN288 4.2 58.7 0.0 N15 B:F7N404 4.3 53.6 1.0 HG21 B:VAL289 4.3 58.6 0.0 HG21 B:ILE40 4.4 81.8 0.0 HA B:VAL37 4.4 99.8 0.0 HA2 B:GLY41 4.4 72.1 0.0 CG2 B:ILE40 4.4 81.8 1.0 HD11 B:LEU45 4.5 68.0 0.0 CA B:VAL289 4.6 55.9 1.0 CB B:VAL37 4.6 0.1 1.0 C13 B:F7N404 4.6 53.8 1.0 H B:GLY41 4.7 73.3 0.0 N B:VAL289 4.7 57.0 1.0 HD23 B:LEU44 4.7 75.3 0.0 HB2 B:GLN288 4.7 58.7 0.0 CB B:VAL289 4.7 59.3 1.0 CB B:ILE40 4.8 80.9 1.0 N B:GLY41 4.8 73.3 1.0 C B:GLN288 4.9 60.9 1.0 C14 B:F7N404 4.9 53.8 1.0 CA B:VAL37 4.9 99.8 1.0 CB B:GLN288 4.9 58.7 1.0 H B:VAL289 5.0 57.0 0.0 C B:VAL37 5.0 99.7 1.0 HA3 B:GLY41 5.0 72.1 0.0 CA B:GLY41 5.0 72.1 1.0

A.K.Apel, R.K.Y.Cheng, C.S.Tautermann, M.Brauchle, C.Y.Huang, A.Pautsch, M.Hennig, H.Nar, G.Schnapp. Crystal Structure of Cc Chemokine Receptor 2A in Complex with An Orthosteric Antagonist Provides Insights For the Design of Selective Antagonists. Structure V. 27 427 2019.
ISSN: ISSN 1878-4186
PubMed: 30581043
DOI: 10.1016/J.STR.2018.10.027