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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: Tue Jul 15 02:59:38 2025

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