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Fluorine in PDB 7zls: Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13

Protein crystallography data

The structure of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13, PDB code: 7zls was solved by S.Ramachandran, A.Ciulli, N.Makukhin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.18 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.549, 172.641, 185.475, 90, 90, 90
R / Rfree (%) 20.2 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 (pdb code 7zls). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13, PDB code: 7zls:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7zls

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Fluorine binding site 1 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:43.7
occ:1.00
 F08 A:JH9202 0.0 43.7 1.0
C07 A:JH9202 1.4 42.3 1.0
C06 A:JH9202 2.4 37.0 1.0
C09 A:JH9202 2.4 41.6 1.0
CG2 J:ILE109 3.4 58.2 1.0
C05 A:JH9202 3.6 37.2 1.0
C10 A:JH9202 3.6 38.0 1.0
CD A:LYS59 3.6 46.7 1.0
CB A:LYS59 3.7 42.9 1.0
CG2 A:VAL55 3.7 37.7 1.0
O A:HOH342 3.8 41.4 1.0
O A:VAL55 3.8 39.8 1.0
CG A:LYS59 4.0 41.4 1.0
C04 A:JH9202 4.1 40.4 1.0
C A:VAL55 4.3 42.7 1.0
CA A:ASN56 4.6 42.6 1.0
N A:ASN56 4.7 40.2 1.0
CB A:VAL55 4.7 41.0 1.0
O J:HOH365 4.7 45.0 1.0
CG1 A:VAL55 4.7 41.0 1.0
CE A:LYS59 4.8 61.0 1.0
ND2 A:ASN94 4.8 33.6 1.0
CB J:ILE109 4.8 58.1 1.0
CA A:LYS59 4.9 42.3 1.0

Fluorine binding site 2 out of 8 in 7zls

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Fluorine binding site 2 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:48.6
occ:1.00
 F20 A:JH9202 0.0 48.6 1.0
C19 A:JH9202 1.4 47.0 1.0
C21 A:JH9202 2.4 50.0 1.0
C18 A:JH9202 2.4 44.9 1.0
C22 A:JH9202 2.8 53.8 1.0
N A:LEU150 3.2 49.8 1.0
CA A:LEU150 3.2 45.6 1.0
C A:HIS149 3.4 59.8 1.0
CB A:LEU150 3.4 44.6 1.0
C23 A:JH9202 3.5 56.5 1.0
O A:HIS149 3.5 58.2 1.0
C25 A:JH9202 3.6 46.5 1.0
C17 A:JH9202 3.6 41.2 1.0
CD1 A:LEU150 3.7 43.0 1.0
O A:VAL148 3.8 73.3 1.0
CD2 A:LEU95 3.9 37.9 1.0
C16 A:JH9202 4.1 44.8 1.0
O A:HOH334 4.1 45.3 1.0
CG A:LEU150 4.2 44.6 1.0
CA A:HIS149 4.2 62.5 1.0
C A:VAL148 4.3 72.2 1.0
C24 A:JH9202 4.3 61.0 1.0
N A:HIS149 4.5 62.6 1.0
C A:LEU150 4.7 48.2 1.0
CB A:VAL148 4.8 64.6 1.0
CG A:LEU95 4.8 35.1 1.0
CB A:LEU95 4.9 33.5 1.0
CD2 A:LEU150 5.0 45.3 1.0

Fluorine binding site 3 out of 8 in 7zls

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Fluorine binding site 3 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:44.0
occ:1.00
 F08 D:JH9201 0.0 44.0 1.0
C07 D:JH9201 1.4 45.0 1.0
C09 D:JH9201 2.4 43.3 1.0
C06 D:JH9201 2.4 43.4 1.0
OD1 D:ASN56 3.1 58.1 1.0
OG G:SER78 3.4 55.4 1.0
CG2 D:VAL55 3.4 43.1 1.0
C10 D:JH9201 3.6 44.8 1.0
O D:VAL55 3.6 44.5 1.0
C05 D:JH9201 3.6 41.0 1.0
CD D:LYS59 3.8 50.1 1.0
CB D:LYS59 3.8 47.7 1.0
C D:VAL55 4.0 43.9 1.0
O D:HOH326 4.0 42.3 1.0
C04 D:JH9201 4.1 42.2 1.0
CG1 D:VAL55 4.1 46.1 1.0
CA D:ASN56 4.2 48.0 1.0
CE1 G:HIS77 4.2 47.2 1.0
CG D:ASN56 4.2 57.4 1.0
N D:ASN56 4.2 41.2 1.0
CB D:VAL55 4.3 42.1 1.0
CG D:LYS59 4.3 44.5 1.0
CE D:LYS59 4.5 55.8 1.0
NZ D:LYS59 4.6 58.5 1.0
NE2 G:HIS77 4.6 43.5 1.0
ND1 G:HIS77 4.6 40.2 1.0
CB G:SER78 4.7 55.4 1.0
CA D:VAL55 4.7 46.3 1.0
CB D:ASN56 4.8 52.0 1.0
N G:SER78 4.8 51.1 1.0
ND2 D:ASN94 4.9 42.9 1.0

Fluorine binding site 4 out of 8 in 7zls

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Fluorine binding site 4 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:83.1
occ:1.00
 F20 D:JH9201 0.0 83.1 1.0
C19 D:JH9201 1.4 74.1 1.0
C21 D:JH9201 2.4 68.8 1.0
C18 D:JH9201 2.4 68.3 1.0
C22 D:JH9201 2.8 72.5 1.0
N D:LEU150 3.3 97.0 1.0
CA D:LEU150 3.4 90.9 1.0
CB D:LEU150 3.5 87.3 1.0
C25 D:JH9201 3.6 65.7 1.0
C17 D:JH9201 3.7 60.1 1.0
C D:HIS149 3.7 102.7 1.0
O D:VAL148 3.9 117.8 1.0
C16 D:JH9201 4.2 59.1 1.0
CA D:HIS149 4.2 109.5 1.0
CD2 D:LEU95 4.2 54.7 1.0
O D:HIS149 4.3 100.8 1.0
O D:HOH320 4.3 70.4 1.0
C D:VAL148 4.5 113.5 1.0
N D:HIS149 4.8 109.6 1.0
CG D:LEU150 4.8 83.8 1.0
C D:LEU150 4.9 89.8 1.0

Fluorine binding site 5 out of 8 in 7zls

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Fluorine binding site 5 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F201

b:49.3
occ:1.00
 F08 J:JH9201 0.0 49.3 1.0
C07 J:JH9201 1.4 41.4 1.0
C09 J:JH9201 2.4 41.2 1.0
C06 J:JH9201 2.4 38.6 1.0
CG2 A:ILE109 3.3 49.2 1.0
CB J:LYS59 3.6 41.6 1.0
C05 J:JH9201 3.6 37.5 1.0
C10 J:JH9201 3.6 40.5 1.0
O J:HOH333 3.7 44.2 1.0
CD J:LYS59 3.7 46.1 1.0
CG2 J:VAL55 3.8 42.8 1.0
O J:VAL55 3.8 38.6 1.0
CG J:LYS59 3.9 43.2 1.0
C04 J:JH9201 4.1 38.0 1.0
C J:VAL55 4.3 42.3 1.0
CA J:ASN56 4.6 44.1 1.0
CB A:ILE109 4.7 52.2 1.0
CG1 J:VAL55 4.7 40.6 1.0
N J:ASN56 4.7 41.3 1.0
O A:HOH365 4.7 48.7 1.0
CB J:VAL55 4.7 39.7 1.0
ND2 J:ASN94 4.8 37.4 1.0
OD1 J:ASN56 4.8 59.0 1.0
CA J:LYS59 4.9 41.7 1.0
CE J:LYS59 5.0 61.7 1.0

Fluorine binding site 6 out of 8 in 7zls

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Fluorine binding site 6 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:F201

b:54.7
occ:1.00
 F20 J:JH9201 0.0 54.7 1.0
C19 J:JH9201 1.4 52.8 1.0
C18 J:JH9201 2.4 49.2 1.0
C21 J:JH9201 2.4 53.1 1.0
C22 J:JH9201 2.9 60.2 1.0
CA J:LEU150 3.3 48.6 1.0
N J:LEU150 3.3 50.2 1.0
CB J:LEU150 3.4 51.8 1.0
C23 J:JH9201 3.4 62.6 1.0
C J:HIS149 3.5 58.6 1.0
C17 J:JH9201 3.6 44.2 1.0
C25 J:JH9201 3.6 48.1 1.0
O J:HIS149 3.6 57.5 1.0
CD1 J:LEU150 3.7 45.3 1.0
CD2 J:LEU95 3.9 46.0 1.0
O J:VAL148 4.0 73.5 1.0
CG J:LEU150 4.1 50.0 1.0
C16 J:JH9201 4.1 48.5 1.0
CG1 J:VAL148 4.2 63.3 1.0
C J:VAL148 4.3 74.8 1.0
CA J:HIS149 4.4 63.2 1.0
N J:HIS149 4.5 64.2 1.0
CB J:VAL148 4.6 69.9 1.0
C24 J:JH9201 4.7 71.7 1.0
C J:LEU150 4.8 52.5 1.0
CD2 J:LEU150 4.8 51.4 1.0
CG J:LEU95 4.9 42.1 1.0
CB J:LEU95 4.9 39.0 1.0
O J:HOH362 4.9 54.3 1.0

Fluorine binding site 7 out of 8 in 7zls

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Fluorine binding site 7 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F201

b:52.2
occ:1.00
 F08 G:JH9201 0.0 52.2 1.0
C07 G:JH9201 1.4 47.9 1.0
C06 G:JH9201 2.4 47.6 1.0
C09 G:JH9201 2.4 44.0 1.0
O G:VAL55 3.5 44.2 1.0
CD G:LYS59 3.5 52.7 1.0
CB G:LYS59 3.6 46.3 1.0
C05 G:JH9201 3.6 46.3 1.0
C10 G:JH9201 3.7 46.6 1.0
CG2 G:VAL55 3.8 40.1 1.0
O G:HOH321 3.9 42.6 1.0
C G:VAL55 4.0 42.5 1.0
CG G:LYS59 4.0 43.2 1.0
CA G:ASN56 4.0 46.9 1.0
ND2 G:ASN56 4.1 68.4 1.0
C04 G:JH9201 4.1 45.6 1.0
CG G:ASN56 4.1 64.3 1.0
NZ G:LYS59 4.2 68.1 1.0
N G:ASN56 4.3 40.0 1.0
OD1 G:ASN56 4.3 71.6 1.0
CE G:LYS59 4.3 58.6 1.0
CG1 G:VAL55 4.7 43.8 1.0
CB G:VAL55 4.7 41.5 1.0
CB G:ASN56 4.7 50.9 1.0
CA G:LYS59 4.8 44.0 1.0
ND2 G:ASN94 4.9 38.4 1.0
CA G:VAL55 4.9 43.4 1.0
CG1 D:VAL148 4.9 103.8 1.0

Fluorine binding site 8 out of 8 in 7zls

Go back to Fluorine Binding Sites List in 7zls
Fluorine binding site 8 out of 8 in the Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Co-Crystal Structure of SOCS2:Elonginb:Elonginc in Complex with Compound 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F201

b:60.9
occ:1.00
 F20 G:JH9201 0.0 60.9 1.0
C19 G:JH9201 1.4 58.8 1.0
C21 G:JH9201 2.4 56.3 1.0
C18 G:JH9201 2.4 51.4 1.0
C22 G:JH9201 2.8 57.9 1.0
CB G:LEU150 3.4 51.7 1.0
CA G:LEU150 3.4 57.6 1.0
N G:LEU150 3.4 62.3 1.0
CD2 G:LEU95 3.6 44.7 1.0
C25 G:JH9201 3.6 55.7 1.0
C17 G:JH9201 3.7 50.1 1.0
C G:HIS149 3.7 71.4 1.0
CD1 G:LEU150 4.0 47.8 1.0
O G:HIS149 4.1 69.3 1.0
C16 G:JH9201 4.1 52.8 1.0
CG G:LEU150 4.3 45.9 1.0
O G:HOH335 4.4 50.4 1.0
CA G:HIS149 4.5 78.0 1.0
CG G:LEU95 4.7 41.1 1.0
CB G:LEU95 4.8 39.6 1.0
C G:LEU150 4.8 52.6 1.0

Reference:

S.Ramachandran, A.Ciulli, N.Makukhin. Structure-Based Design of A Phosphotyrosine-Masked, Cell-Penetrant Small Molecule Covalently Targeting CYS111 on the E3 Ligase SOCS2 To Be Published.
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