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Fluorine in PDB 4iti: Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog

Enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog

All present enzymatic activity of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog, PDB code: 4iti was solved by T.Xie, W.Peng, Y.Liu, C.Yan, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.27 / 2.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.630, 91.407, 103.325, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 26.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog (pdb code 4iti). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog, PDB code: 4iti:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 1 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


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 RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:86.4
occ:1.00
 F31 A:1HW301 0.0 86.4 1.0
C28 A:1HW301 1.3 86.1 1.0
F30 A:1HW301 2.2 86.0 1.0
F29 A:1HW301 2.2 85.3 1.0
O27 A:1HW301 2.2 86.7 1.0
C17 A:1HW301 3.2 86.5 1.0
CG1 A:VAL134 3.2 56.9 1.0
OG A:SER161 3.4 76.1 1.0
C18 A:1HW301 3.5 85.8 1.0
CB A:SER161 3.8 76.9 1.0
CE A:MET67 3.9 79.9 1.0
CD1 A:LEU70 4.0 80.2 1.0
CD2 A:LEU129 4.3 66.9 1.0
CA A:HIS136 4.4 61.4 1.0
CD1 A:LEU129 4.5 64.0 1.0
C16 A:1HW301 4.5 87.1 1.0
CB A:VAL134 4.7 59.7 1.0
N A:HIS136 4.8 63.9 1.0
O A:ILE135 4.8 68.5 0.0
O A:ILE135 4.8 68.5 1.0
C19 A:1HW301 4.8 85.5 1.0
C A:ILE135 4.9 69.4 0.0
C A:ILE135 4.9 69.4 1.0
CB A:HIS136 4.9 59.3 1.0
CD2 A:HIS136 4.9 58.8 1.0
CG A:LEU129 5.0 68.5 1.0
F26 A:1HW301 5.0 87.8 1.0

Fluorine binding site 2 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 2 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


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 RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:85.3
occ:1.00
 F29 A:1HW301 0.0 85.3 1.0
C28 A:1HW301 1.3 86.1 1.0
OG A:SER161 2.1 76.1 1.0
F30 A:1HW301 2.2 86.0 1.0
F31 A:1HW301 2.2 86.4 1.0
O27 A:1HW301 2.2 86.7 1.0
C18 A:1HW301 2.3 85.8 1.0
C17 A:1HW301 2.6 86.5 1.0
CB A:SER161 3.2 76.9 1.0
CB A:ASP156 3.3 60.6 1.0
OD2 A:ASP156 3.5 62.9 1.0
C19 A:1HW301 3.6 85.5 1.0
CG A:ASP156 3.8 62.6 1.0
C16 A:1HW301 4.0 87.1 1.0
CD2 A:HIS136 4.2 58.8 1.0
CE A:MET67 4.3 79.9 1.0
CG A:HIS136 4.4 59.6 1.0
CA A:HIS136 4.4 61.4 1.0
CA A:SER161 4.5 76.6 1.0
NE2 A:HIS136 4.5 58.8 1.0
CA A:ASP156 4.6 60.9 1.0
C14 A:1HW301 4.7 86.1 1.0
CE2 A:PHE162 4.7 67.8 1.0
O A:HIS136 4.7 58.6 1.0
N A:SER161 4.8 73.8 1.0
F26 A:1HW301 4.8 87.8 1.0
C15 A:1HW301 4.8 86.9 1.0
CB A:HIS136 4.8 59.3 1.0
OD1 A:ASP156 4.9 62.8 1.0
ND1 A:HIS136 4.9 58.3 1.0
N A:ASP156 4.9 61.3 1.0
CE1 A:HIS136 5.0 57.8 1.0

Fluorine binding site 3 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 3 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


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 RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:86.0
occ:1.00
 F30 A:1HW301 0.0 86.0 1.0
C28 A:1HW301 1.3 86.1 1.0
F29 A:1HW301 2.2 85.3 1.0
F31 A:1HW301 2.2 86.4 1.0
O27 A:1HW301 2.2 86.7 1.0
CD2 A:HIS136 2.9 58.8 1.0
CA A:HIS136 2.9 61.4 1.0
CG A:HIS136 2.9 59.6 1.0
CB A:HIS136 3.0 59.3 1.0
C17 A:1HW301 3.4 86.5 1.0
OG A:SER161 3.5 76.1 1.0
N A:HIS136 3.7 63.9 1.0
CB A:SER161 3.8 76.9 1.0
NE2 A:HIS136 3.8 58.8 1.0
ND1 A:HIS136 3.9 58.3 1.0
C18 A:1HW301 3.9 85.8 1.0
CD1 A:LEU129 4.0 64.0 1.0
C A:HIS136 4.0 60.5 1.0
O A:HIS136 4.2 58.6 1.0
CE1 A:HIS136 4.3 57.8 1.0
C A:ILE135 4.4 69.4 0.0
C A:ILE135 4.4 69.4 1.0
O A:ILE135 4.5 68.5 0.0
O A:ILE135 4.5 68.5 1.0
C16 A:1HW301 4.6 87.1 1.0
CG1 A:VAL134 4.6 56.9 1.0
CB A:ASP156 4.7 60.6 1.0
F26 A:1HW301 4.8 87.8 1.0
OD2 A:ASP156 4.9 62.9 1.0
CG A:LEU129 5.0 68.5 1.0
CD2 A:LEU129 5.0 66.9 1.0

Fluorine binding site 4 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 4 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


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 RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:87.8
occ:1.00
 F26 A:1HW301 0.0 87.8 1.0
C16 A:1HW301 1.3 87.1 1.0
C15 A:1HW301 2.4 86.9 1.0
C17 A:1HW301 2.5 86.5 1.0
O A:ILE154 2.8 63.1 1.0
O27 A:1HW301 2.8 86.7 1.0
CB A:VAL75 3.4 71.0 1.0
C A:ILE154 3.5 62.0 1.0
C14 A:1HW301 3.6 86.1 1.0
C18 A:1HW301 3.7 85.8 1.0
CG1 A:VAL75 3.7 71.3 1.0
CG2 A:ILE154 3.8 65.2 1.0
CB A:ILE154 3.9 64.3 1.0
CA A:VAL75 4.0 70.9 1.0
C19 A:1HW301 4.1 85.5 1.0
N A:ALA155 4.2 61.6 1.0
C28 A:1HW301 4.3 86.1 1.0
CA A:ALA155 4.3 62.8 1.0
CA A:ILE154 4.3 64.2 1.0
CD1 A:LEU129 4.3 64.0 1.0
C A:ALA155 4.5 61.9 1.0
N A:VAL76 4.6 73.5 1.0
CD2 A:LEU129 4.6 66.9 1.0
CG2 A:VAL75 4.6 73.5 1.0
O A:ALA155 4.8 63.5 1.0
C A:VAL75 4.8 69.5 1.0
F30 A:1HW301 4.8 86.0 1.0
F29 A:1HW301 4.8 85.3 1.0
C11 A:1HW301 4.8 85.8 1.0
C8 A:1HW301 4.9 87.5 1.0
F31 A:1HW301 5.0 86.4 1.0
N A:ILE154 5.0 65.2 1.0

Fluorine binding site 5 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 5 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


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 RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:94.9
occ:1.00
 F31 B:1HW301 0.0 94.9 1.0
C28 B:1HW301 1.3 94.2 1.0
F29 B:1HW301 2.2 94.4 1.0
F30 B:1HW301 2.2 93.2 1.0
O27 B:1HW301 2.2 94.5 1.0
OG B:SER161 2.9 77.8 1.0
CG1 B:VAL134 3.2 70.9 1.0
CB B:SER161 3.3 77.7 1.0
C17 B:1HW301 3.3 94.8 1.0
C18 B:1HW301 3.6 95.5 1.0
CA B:HIS136 3.8 71.8 1.0
O B:ILE135 4.0 80.6 1.0
N B:HIS136 4.2 72.3 1.0
C B:ILE135 4.2 78.8 1.0
CD2 B:HIS136 4.3 70.0 1.0
CB B:HIS136 4.4 69.8 1.0
CB B:VAL134 4.4 72.9 1.0
CG B:HIS136 4.5 72.7 1.0
C16 B:1HW301 4.7 94.7 1.0
OD2 B:ASP156 4.7 76.4 1.0
CA B:SER161 4.8 79.6 1.0
O B:HIS136 4.8 75.9 1.0
C B:HIS136 4.8 72.4 1.0
N B:ILE135 5.0 78.4 1.0
C B:VAL134 5.0 69.9 1.0
CD2 B:LEU129 5.0 61.9 1.0
CD1 B:LEU129 5.0 60.1 1.0

Fluorine binding site 6 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 6 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


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 RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:94.4
occ:1.00
 F29 B:1HW301 0.0 94.4 1.0
C28 B:1HW301 1.3 94.2 1.0
F31 B:1HW301 2.2 94.9 1.0
F30 B:1HW301 2.2 93.2 1.0
O27 B:1HW301 2.2 94.5 1.0
C18 B:1HW301 2.3 95.5 1.0
OG B:SER161 2.4 77.8 1.0
C17 B:1HW301 2.5 94.8 1.0
CB B:ASP156 3.0 72.6 1.0
OD2 B:ASP156 3.1 76.4 1.0
CB B:SER161 3.4 77.7 1.0
CG B:ASP156 3.5 76.5 1.0
C19 B:1HW301 3.6 96.2 1.0
CD2 B:HIS136 3.6 70.0 1.0
C16 B:1HW301 3.9 94.7 1.0
NE2 B:HIS136 4.0 70.9 1.0
CG B:HIS136 4.1 72.7 1.0
CA B:ASP156 4.3 73.4 1.0
CA B:HIS136 4.4 71.8 1.0
N B:ASP156 4.6 71.9 1.0
CE1 B:HIS136 4.6 71.3 1.0
O B:ALA155 4.6 56.0 1.0
C14 B:1HW301 4.6 96.2 1.0
OD1 B:ASP156 4.6 76.7 1.0
ND1 B:HIS136 4.7 70.4 1.0
O B:HIS136 4.7 75.9 1.0
CA B:SER161 4.7 79.6 1.0
CB B:HIS136 4.7 69.8 1.0
F26 B:1HW301 4.7 94.2 1.0
C15 B:1HW301 4.7 95.4 1.0
C B:ALA155 4.8 55.4 1.0
N B:SER161 4.8 81.5 1.0

Fluorine binding site 7 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 7 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:93.2
occ:1.00
 F30 B:1HW301 0.0 93.2 1.0
C28 B:1HW301 1.3 94.2 1.0
F29 B:1HW301 2.2 94.4 1.0
F31 B:1HW301 2.2 94.9 1.0
O27 B:1HW301 2.2 94.5 1.0
CD2 B:HIS136 2.3 70.0 1.0
CG B:HIS136 2.7 72.7 1.0
CB B:HIS136 3.1 69.8 1.0
C17 B:1HW301 3.3 94.8 1.0
CA B:HIS136 3.3 71.8 1.0
NE2 B:HIS136 3.3 70.9 1.0
ND1 B:HIS136 3.8 70.4 1.0
C18 B:1HW301 3.9 95.5 1.0
CE1 B:HIS136 4.1 71.3 1.0
OG B:SER161 4.1 77.8 1.0
N B:HIS136 4.1 72.3 1.0
C16 B:1HW301 4.3 94.7 1.0
CD1 B:LEU129 4.3 60.1 1.0
C B:HIS136 4.4 72.4 1.0
F26 B:1HW301 4.4 94.2 1.0
CB B:SER161 4.5 77.7 1.0
O B:ALA155 4.5 56.0 1.0
O B:HIS136 4.5 75.9 1.0
CB B:ASP156 4.6 72.6 1.0
CG2 B:ILE154 4.7 56.7 1.0
OD2 B:ASP156 4.7 76.4 1.0
C B:ILE135 4.8 78.8 1.0
O B:ILE135 4.9 80.6 1.0
CG B:ASP156 4.9 76.5 1.0

Fluorine binding site 8 out of 8 in 4iti

Go back to Fluorine Binding Sites List in 4iti
Fluorine binding site 8 out of 8 in the Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of RIP1 Kinase in Complex with Necrostatin-3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:94.2
occ:1.00
 F26 B:1HW301 0.0 94.2 1.0
C16 B:1HW301 1.3 94.7 1.0
C15 B:1HW301 2.4 95.4 1.0
C17 B:1HW301 2.5 94.8 1.0
O27 B:1HW301 2.9 94.5 1.0
CG1 B:VAL75 3.1 70.9 1.0
CB B:VAL75 3.5 67.6 1.0
O B:ILE154 3.6 62.9 1.0
C14 B:1HW301 3.6 96.2 1.0
C18 B:1HW301 3.7 95.5 1.0
CD1 B:LEU129 3.8 60.1 1.0
C B:ILE154 4.1 59.4 1.0
C19 B:1HW301 4.1 96.2 1.0
CG2 B:ILE154 4.2 56.7 1.0
C28 B:1HW301 4.2 94.2 1.0
CD2 B:LEU129 4.2 61.9 1.0
CA B:VAL75 4.3 66.7 1.0
CB B:ILE154 4.3 57.6 1.0
F30 B:1HW301 4.4 93.2 1.0
CG B:LEU129 4.6 62.8 1.0
N B:ALA155 4.6 52.8 1.0
CG2 B:VAL75 4.7 74.1 1.0
F29 B:1HW301 4.7 94.4 1.0
CA B:ALA155 4.7 55.5 1.0
C8 B:1HW301 4.8 98.6 1.0
CA B:ILE154 4.8 60.0 1.0
C11 B:1HW301 4.9 97.2 1.0
N B:VAL76 4.9 75.5 1.0
C B:ALA155 5.0 55.4 1.0

Reference:

T.Xie, W.Peng, Y.Liu, C.Yan, J.Maki, A.Degterev, J.Yuan, Y.Shi. Structural Basis of RIP1 Inhibition By Necrostatins. Structure V. 21 493 2013.
ISSN: ISSN 0969-2126
PubMed: 23473668
DOI: 10.1016/J.STR.2013.01.016
Page generated: Sun Dec 13 12:04:46 2020

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