Atomistry » Fluorine » PDB 5ci0-5dde » 5ddc
Atomistry »
  Fluorine »
    PDB 5ci0-5dde »
      5ddc »

Fluorine in PDB 5ddc: Menin in Complex with Mi-2-3

Protein crystallography data

The structure of Menin in Complex with Mi-2-3, PDB code: 5ddc was solved by J.Pollock, B.Dmitry, T.Cierpicki, J.Grembecka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.74 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.445, 80.253, 124.456, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.4

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 5ddc

Go back to Fluorine Binding Sites List in 5ddc
Fluorine binding site 1 out of 6 in the Menin in Complex with Mi-2-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Menin in Complex with Mi-2-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:9.8
occ:1.00
 FAA A:59V601 0.0 9.8 1.0
CBB A:59V601 1.3 7.9 1.0
FAB A:59V601 2.2 7.1 1.0
FAC A:59V601 2.2 8.1 1.0
CAM A:59V601 2.4 6.7 1.0
CAT A:59V601 2.9 6.8 1.0
O A:HOH1119 3.1 19.4 1.0
C1 A:DMS604 3.4 22.4 0.5
OG A:SER155 3.4 7.4 1.0
CAH A:59V601 3.4 6.4 1.0
O A:HOH1165 3.6 23.2 1.0
CB A:SER155 3.6 5.5 1.0
S A:DMS602 3.6 10.9 0.5
O A:HOH1138 3.8 40.3 1.0
O A:DMS602 3.8 12.2 0.5
O A:HOH857 3.9 12.4 1.0
SAS A:59V601 4.0 8.2 1.0
C2 A:DMS602 4.1 12.5 0.5
C5 A:59V601 4.4 6.9 1.0
C4 A:59V601 4.7 7.9 1.0
CE1 A:PHE238 4.7 5.5 1.0
N A:HIS181 4.8 3.6 1.0
S A:DMS604 4.9 22.5 0.5
C A:ASP180 5.0 4.8 1.0
CA A:SER155 5.0 5.2 1.0

Fluorine binding site 2 out of 6 in 5ddc

Go back to Fluorine Binding Sites List in 5ddc
Fluorine binding site 2 out of 6 in the Menin in Complex with Mi-2-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Menin in Complex with Mi-2-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:7.1
occ:1.00
 FAB A:59V601 0.0 7.1 1.0
CBB A:59V601 1.3 7.9 1.0
FAA A:59V601 2.2 9.8 1.0
FAC A:59V601 2.2 8.1 1.0
CAM A:59V601 2.4 6.7 1.0
C A:HIS181 3.0 5.8 1.0
CA A:HIS181 3.0 3.7 1.0
N A:HIS181 3.1 3.6 1.0
O A:HOH1165 3.1 23.2 1.0
O A:HIS181 3.2 5.1 1.0
N A:ALA182 3.5 5.3 1.0
C A:ASP180 3.5 4.8 1.0
O A:HOH1119 3.6 19.4 1.0
CAT A:59V601 3.7 6.8 1.0
CB A:SER155 3.8 5.5 1.0
O A:HOH728 3.8 20.3 1.0
O A:ASP180 3.9 6.6 1.0
CB A:ALA182 4.0 4.8 1.0
CA A:ALA182 4.3 3.1 1.0
OG A:SER155 4.4 7.4 1.0
CA A:ASP180 4.4 5.3 1.0
CB A:HIS181 4.5 3.7 1.0
O A:HOH857 4.6 12.4 1.0
CAH A:59V601 4.7 6.4 1.0
SAS A:59V601 4.7 8.2 1.0
CA A:SER155 4.8 5.2 1.0
N A:ASP180 4.9 4.6 1.0
O A:SER178 5.0 4.9 1.0

Fluorine binding site 3 out of 6 in 5ddc

Go back to Fluorine Binding Sites List in 5ddc
Fluorine binding site 3 out of 6 in the Menin in Complex with Mi-2-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Menin in Complex with Mi-2-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:8.1
occ:1.00
 FAC A:59V601 0.0 8.1 1.0
CBB A:59V601 1.3 7.9 1.0
FAA A:59V601 2.2 9.8 1.0
FAB A:59V601 2.2 7.1 1.0
CAM A:59V601 2.4 6.7 1.0
CAT A:59V601 2.9 6.8 1.0
SAS A:59V601 3.1 8.2 1.0
CB A:SER155 3.4 5.5 1.0
CD2 A:LEU177 3.5 6.4 1.0
CE1 A:PHE238 3.6 5.5 1.0
CB A:ALA182 3.8 4.8 1.0
O A:HIS181 3.8 5.1 1.0
OG A:SER155 3.9 7.4 1.0
CAH A:59V601 4.0 6.4 1.0
C A:HIS181 4.1 5.8 1.0
CZ A:PHE238 4.2 6.2 1.0
C1 A:DMS604 4.3 22.4 0.5
S A:DMS602 4.3 10.9 0.5
N A:ALA182 4.4 5.3 1.0
C4 A:59V601 4.5 7.9 1.0
CA A:ALA182 4.5 3.1 1.0
CD1 A:PHE238 4.6 5.1 1.0
N A:HIS181 4.7 3.6 1.0
CA A:HIS181 4.7 3.7 1.0
CG A:LEU177 4.8 7.0 1.0
CA A:SER155 4.8 5.2 1.0
C5 A:59V601 4.8 6.9 1.0
O A:HOH1165 4.9 23.2 1.0
O A:SER178 4.9 4.9 1.0
C2 A:DMS602 4.9 12.5 0.5
O A:HOH1119 4.9 19.4 1.0
CB A:LEU177 5.0 6.4 1.0

Fluorine binding site 4 out of 6 in 5ddc

Go back to Fluorine Binding Sites List in 5ddc
Fluorine binding site 4 out of 6 in the Menin in Complex with Mi-2-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Menin in Complex with Mi-2-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:20.0
occ:1.00
 FAE A:59V601 0.0 20.0 1.0
CBC A:59V601 1.3 17.1 0.9
FAD A:59V601 2.2 15.0 0.8
FAF A:59V601 2.2 21.2 1.0
CAV A:59V601 2.3 9.2 1.0
SAR A:59V601 3.3 10.9 1.0
NAQ A:59V601 3.3 12.1 1.0
CB A:MET322 3.4 7.9 0.5
CB A:MET322 3.6 5.1 0.5
O A:HOH1000 3.8 24.1 1.0
O A:HOH716 3.9 18.2 0.5
CD1 A:TYR319 3.9 6.8 1.0
OE2 A:GLU363 4.1 45.2 0.5
CE1 A:TYR319 4.2 7.1 1.0
CG A:MET322 4.2 17.4 0.5
SD A:MET322 4.2 4.7 0.5
NAP A:59V601 4.3 14.1 1.0
C A:MET322 4.3 6.9 1.0
CAU A:59V601 4.4 9.2 1.0
CA A:MET322 4.5 5.6 0.5
O A:MET322 4.5 5.7 1.0
CG A:MET322 4.5 5.7 0.5
CA A:MET322 4.6 4.4 0.5
N A:TYR323 4.6 5.5 1.0
CD A:GLU363 4.7 25.6 0.5
O A:HOH1012 4.7 22.9 1.0
CG A:TYR319 4.8 4.4 1.0
SD A:MET322 4.8 15.5 0.5
O A:HOH1073 4.9 19.9 1.0
OE1 A:GLU363 4.9 21.8 0.5

Fluorine binding site 5 out of 6 in 5ddc

Go back to Fluorine Binding Sites List in 5ddc
Fluorine binding site 5 out of 6 in the Menin in Complex with Mi-2-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Menin in Complex with Mi-2-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:21.2
occ:1.00
 FAF A:59V601 0.0 21.2 1.0
CBC A:59V601 1.3 17.1 0.9
FAD A:59V601 2.2 15.0 0.8
FAE A:59V601 2.2 20.0 1.0
CAV A:59V601 2.3 9.2 1.0
NAQ A:59V601 2.7 12.1 1.0
O A:HOH1073 3.1 19.9 1.0
O A:HOH1000 3.2 24.1 1.0
O A:HOH883 3.4 17.1 1.0
CA A:TYR323 3.6 6.1 1.0
O A:MET322 3.7 5.7 1.0
N A:TYR323 3.7 5.5 1.0
C A:MET322 3.7 6.9 1.0
CD1 A:TYR323 3.8 6.4 1.0
SAR A:59V601 3.8 10.9 1.0
CG A:TYR323 4.0 5.5 1.0
NAP A:59V601 4.0 14.1 1.0
CB A:MET322 4.2 7.9 0.5
O A:HOH848 4.2 10.3 1.0
CE1 A:TYR323 4.3 7.9 1.0
CB A:MET322 4.3 5.1 0.5
CB A:TYR323 4.4 6.8 1.0
CAU A:59V601 4.6 9.2 1.0
CA A:MET322 4.6 5.6 0.5
CD2 A:TYR323 4.7 8.1 1.0
CA A:MET322 4.7 4.4 0.5
C A:TYR323 4.8 6.0 1.0
O A:HOH1012 4.9 22.9 1.0
CZ A:TYR323 4.9 7.5 1.0
O A:TYR323 5.0 6.3 1.0

Fluorine binding site 6 out of 6 in 5ddc

Go back to Fluorine Binding Sites List in 5ddc
Fluorine binding site 6 out of 6 in the Menin in Complex with Mi-2-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Menin in Complex with Mi-2-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:15.0
occ:0.80
 FAD A:59V601 0.0 15.0 0.8
CBC A:59V601 1.3 17.1 0.9
FAE A:59V601 2.2 20.0 1.0
FAF A:59V601 2.2 21.2 1.0
CAV A:59V601 2.3 9.2 1.0
CB A:MET322 3.0 7.9 0.5
SAR A:59V601 3.0 10.9 1.0
N A:TYR323 3.0 5.5 1.0
CB A:MET322 3.2 5.1 0.5
O A:TYR319 3.3 6.7 1.0
C A:MET322 3.4 6.9 1.0
NAQ A:59V601 3.5 12.1 1.0
CG A:TYR323 3.6 5.5 1.0
CD2 A:TYR323 3.6 8.1 1.0
CA A:TYR323 3.6 6.1 1.0
CD1 A:TYR319 3.7 6.8 1.0
CB A:TYR319 3.8 5.2 1.0
CA A:MET322 3.8 5.6 0.5
CA A:MET322 3.8 4.4 0.5
CE2 A:TYR323 3.9 8.8 1.0
CD1 A:TYR323 4.0 6.4 1.0
CA A:TYR319 4.0 4.1 1.0
O A:MET322 4.0 5.7 1.0
CG A:TYR319 4.0 4.4 1.0
C A:TYR319 4.0 5.3 1.0
CB A:TYR323 4.1 6.8 1.0
CG A:MET322 4.3 17.4 0.5
CZ A:TYR323 4.3 7.5 1.0
CE1 A:TYR323 4.3 7.9 1.0
CAU A:59V601 4.4 9.2 1.0
NAP A:59V601 4.5 14.1 1.0
N A:MET322 4.5 4.3 1.0
CG A:MET322 4.6 5.7 0.5
CE1 A:TYR319 4.6 7.1 1.0
O A:HOH1000 4.6 24.1 1.0
SD A:MET322 4.9 4.7 0.5

Reference:

J.Pollock, D.Borkin, G.Lund, T.Purohit, E.Dyguda-Kazimierowicz, J.Grembecka, T.Cierpicki. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J.Med.Chem. V. 58 7465 2015.
ISSN: ISSN 0022-2623
PubMed: 26288158
DOI: 10.1021/ACS.JMEDCHEM.5B00975
Page generated: Thu Aug 1 08:42:25 2024

Last articles

Ca in 2YZ4
Ca in 2YOC
Ca in 2YN5
Ca in 2YV9
Ca in 2YV7
Ca in 2YOA
Ca in 2YLJ
Ca in 2YLL
Ca in 2YIK
Ca in 2YKN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy