5AR7 - chain A (model A) | Receptor interacting serine/threonine kinase 2
Structure information
PDB:5AR7
PubMed:26455654
Release date:2015-10-21
Resolution:2.71 Å
 
Kinase:RIPK2
Family:RIPK
Group:TKL
Species:HUMAN
 
Quality Score:7.6
Missing Residues:0
Missing Atoms:0
DFG conformation:out
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.8Å)
 
 
ASP rotation (xDFG.81) :208°
PHE rotation (xDFG.82) :196°
Activation loop position:2.4Å
αC-helix position:18.8Å
 
G-rich loop angle:57.8°
G-rich loop distance:18.1Å
G-rich loop rotation:41.5°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I9
No H-bonds
Binding pocket sequence
UniprotRYLSRGASGTVSSVAVKHLDVLREAEILHKARSYILPILGIGIVTEYMPNGSLNELLHRHNMTPPLLHHDLKTQNILLIADFGLS
Structure:RYLSRGASGTVSSVAVKHLDVLREAEILHKARSYILPILGIGIVTEYMPNGSLNELLHRHNMTPPLLHHDLKTQNILLIADFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: SR8
Ligand Name: 1-(5-TERT-BUTYL-1,2-OXAZOL-3-YL)-3-(4-PYRIDIN-4-YLOXYPHENYL)UREA

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  • LABELS
  • KLIFS residue #
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
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This ligand targets the following (sub)pockets:
Main pockets
Front

Gate

Back

Subpockets
FP-I

FP-II

BP-I-A

BP-I-B

BP-II-in

BP-II-A-in

BP-II-B-in

BP-II-out

BP-II-B

BP-III

BP-IV

BP-V

Kinase-ligand interactions
Hydrophobic Aromatic face-to-face Aromatic face-to-edge H-bond donor H-bond acceptor Ionic positive Ionic negative
I g.l II III αC
1 R
22
2 Y
23
3 L
24
4 S
25
5 R
26
6 G
27
7 A
28
8 S
29
9 G
30
10 T
31
11 V
32
12 S
33
13 S
34
14 V
44
15 A
45
16 V
46
17 K
47
18 H
48
19 L
49
20 D
62
αC b.l IV
21 V
63
22 L
64
23 R
65
24 E
66
25 A
67
26 E
68
27 I
69
28 L
70
29 H
71
30 K
72
31 A
73
32 R
74
33 S
76
34 Y
77
35 I
78
36 L
79
37 P
80
38 I
81
39 L
82
40 G
83
IV V GK hinge linker αD αE
41 I
84
42 G
92
43 I
93
44 V
94
45 T
95
46 E
96
47 Y
97
48 M
98
49 P
99
50 N
100
51 G
101
52 S
102
53 L
103
54 N
104
55 E
105
56 L
106
57 L
107
58 H
108
59 R
109
60 H
136
αE VI c.l VII VIII x
61 N
137
62 M
138
63 T
139
64 P
140
65 P
141
66 L
142
67 L
143
68 H
144
69 H
145
70 D
146
71 L
147
72 K
148
73 T
149
74 Q
150
75 N
151
76 I
152
77 L
153
78 L
154
79 I
162
80 A
163
DFG a.l
81 D
164
82 F
165
83 G
166
84 L
167
85 S
168

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL166031
Bioaffinities: 5 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensSerine/threonine-protein kinase RAF6.66.66.6pIC503
Homo sapiensSerine/threonine-protein kinase RIPK26.56.57.2pIC502