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Iodine in PDB 7ydx: Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962

Enzymatic activity of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962

All present enzymatic activity of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962, PDB code: 7ydx was solved by L.Zhang, Y.Wang, Y.Li, C.Wu, X.Luo, T.Wang, J.Lei, S.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.77 / 2.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.569, 97.53, 132.377, 90, 90, 90
R / Rfree (%) 26 / 28.9

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 (pdb code 7ydx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962, PDB code: 7ydx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 7ydx

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Iodine binding site 1 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:30.0
occ:1.00
 CB A:LYS284 4.0 46.1 1.0
CA A:PHE285 4.0 39.0 1.0
CD2 A:PHE285 4.1 36.2 1.0
C A:LYS284 4.2 51.0 1.0
CB A:GLU259 4.2 51.6 1.0
O A:LYS284 4.2 52.0 1.0
N A:PHE285 4.3 46.2 1.0
CB A:PHE285 4.3 33.4 1.0
CD2 A:PHE288 4.4 46.0 1.0
O A:GLU259 4.6 47.3 1.0
CB A:PHE288 4.6 41.7 1.0
CG A:PHE285 4.7 33.9 1.0
CA A:LYS284 4.7 45.8 1.0
CG A:PHE288 4.7 45.5 1.0
CG A:GLU259 4.8 49.8 1.0
CE A:LYS284 4.9 36.0 1.0
CG A:LYS284 5.0 45.6 1.0
C A:GLU259 5.0 46.5 1.0
CD2 A:LEU263 5.0 26.6 1.0

Iodine binding site 2 out of 7 in 7ydx

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Iodine binding site 2 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:30.0
occ:1.00
 NE A:ARG286 3.3 34.8 1.0
CD A:ARG286 3.6 30.9 1.0
OE2 A:GLU282 3.7 52.6 1.0
CB B:SER73 3.9 31.7 1.0
CA B:SER73 4.2 30.8 1.0
CD A:GLU282 4.3 53.0 1.0
CG A:GLU282 4.4 50.8 1.0
CZ A:ARG286 4.4 36.4 1.0
CB A:ARG286 4.5 32.5 1.0
N B:SER73 4.6 31.3 1.0
CG A:ARG286 4.6 32.3 1.0
NH2 A:ARG286 4.7 39.0 1.0
O A:GLU282 4.7 47.8 1.0
OG B:SER73 5.0 31.6 1.0

Iodine binding site 3 out of 7 in 7ydx

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Iodine binding site 3 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:30.0
occ:1.00
 N A:LEU41 3.8 29.3 1.0
CE1 A:PHE35 3.8 31.0 1.0
CG A:LEU41 3.8 31.4 1.0
CB A:LEU41 4.2 26.4 1.0
CA A:GLY40 4.2 29.6 1.0
CD1 A:LEU41 4.3 30.3 1.0
C A:GLY40 4.5 32.9 1.0
CA A:LEU41 4.6 27.4 1.0
CZ A:PHE35 4.6 29.9 1.0
CD1 A:PHE35 4.6 29.0 1.0
CD2 A:LEU41 4.9 31.9 1.0

Iodine binding site 4 out of 7 in 7ydx

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Iodine binding site 4 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:30.0
occ:1.00
 NH2 B:ARG74 3.6 26.8 1.0
NH1 A:ARG286 3.7 34.8 1.0
CE1 B:HIS151 4.0 27.1 1.0
NH1 B:ARG74 4.1 39.7 1.0
NE2 B:HIS151 4.1 40.8 1.0
CZ B:ARG74 4.3 40.5 1.0
ND1 B:HIS151 4.3 37.2 1.0
CD2 A:LEU290 4.4 45.7 1.0
CD A:ARG286 4.5 30.9 1.0
CD2 B:HIS151 4.6 38.8 1.0
CD1 A:LEU290 4.6 45.5 1.0
CG A:LEU290 4.7 38.5 1.0
CG A:ARG286 4.7 32.3 1.0
CG B:HIS151 4.7 31.9 1.0
CZ A:ARG286 4.8 36.4 1.0
OE1 A:GLU294 4.8 55.1 1.0
CD2 A:LEU120 5.0 21.6 1.0

Iodine binding site 5 out of 7 in 7ydx

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Iodine binding site 5 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:30.0
occ:1.00
 CD1 B:PHE285 3.8 29.3 1.0
CA B:PHE285 4.1 43.6 1.0
O B:LYS284 4.2 45.8 1.0
CB B:LYS284 4.3 41.8 1.0
C B:LYS284 4.3 42.0 1.0
O B:GLU259 4.3 42.8 1.0
CB B:PHE285 4.3 31.5 1.0
N B:PHE285 4.3 42.1 1.0
CB B:GLU259 4.4 44.5 1.0
CB B:LEU263 4.5 40.9 1.0
CG B:PHE285 4.5 31.1 1.0
CD2 B:LEU263 4.6 34.6 1.0
CB B:PHE288 4.6 46.5 1.0
CD2 B:PHE288 4.6 49.5 1.0
CG B:PHE288 4.7 48.4 1.0
CD1 B:LEU263 4.7 37.5 1.0
C B:GLU259 4.7 46.3 1.0
CE1 B:PHE285 4.8 37.6 1.0
CD B:LYS284 4.8 49.7 1.0
CG B:LEU263 4.9 38.9 1.0
CA B:LYS284 5.0 43.6 1.0
CE B:LYS284 5.0 39.9 1.0

Iodine binding site 6 out of 7 in 7ydx

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Iodine binding site 6 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:30.0
occ:1.00
 NE B:ARG286 3.4 38.6 1.0
CD B:ARG286 3.7 31.5 1.0
OE2 B:GLU282 4.1 40.7 1.0
CG B:GLU282 4.2 39.9 1.0
CD B:GLU282 4.2 52.1 1.0
CB B:ARG286 4.3 37.9 1.0
O B:GLU282 4.4 43.7 1.0
CA A:SER73 4.4 26.1 1.0
CB A:SER73 4.4 25.8 1.0
CZ B:ARG286 4.5 40.3 1.0
CA B:GLU283 4.6 43.1 1.0
CG B:ARG286 4.6 34.4 1.0
C B:GLU282 4.6 43.1 1.0
N B:GLU283 4.7 44.4 1.0
N A:SER73 4.7 28.4 1.0
NH2 B:ARG286 4.7 30.5 1.0
CG B:GLU283 4.7 58.7 1.0
O A:HOH407 4.8 35.8 1.0
OE1 B:GLU282 4.9 53.9 1.0

Iodine binding site 7 out of 7 in 7ydx

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Iodine binding site 7 out of 7 in the Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Human RIPK1 Kinase Domain in Complex with Compound Ri-962 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:30.0
occ:1.00
 NH1 B:ARG286 3.1 39.2 1.0
NH2 A:ARG74 3.6 29.3 1.0
NH1 A:ARG74 4.0 29.9 1.0
CE1 A:HIS151 4.1 40.5 1.0
CD2 B:LEU290 4.1 38.7 1.0
NE2 A:HIS151 4.1 42.4 1.0
CZ A:ARG74 4.3 35.6 1.0
CZ B:ARG286 4.4 40.3 1.0
CD B:ARG286 4.4 31.5 1.0
CG B:ARG286 4.5 34.4 1.0
CD2 B:LEU120 4.5 33.6 1.0
ND1 A:HIS151 4.5 37.5 1.0
CG B:LEU290 4.6 49.0 1.0
OE2 B:GLU294 4.6 39.3 1.0
CD2 A:HIS151 4.6 38.7 1.0
CD1 B:LEU290 4.8 51.8 1.0
NE B:ARG286 4.8 38.6 1.0
CG A:HIS151 4.9 38.5 1.0

Reference:

Y.Li, L.Zhang, Y.Wang, J.Zou, R.Yang, X.Luo, C.Wu, W.Yang, C.Tian, H.Xu, F.Wang, X.Yang, L.Li, S.Yang. Generative Deep Learning Enables the Discovery of A Potent and Selective RIPK1 Inhibitor. Nat Commun V. 13 6891 2022.
ISSN: ESSN 2041-1723
PubMed: 36371441
DOI: 10.1038/S41467-022-34692-W
Page generated: Tue Apr 25 21:08:20 2023

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