3WE4 - chain A | Ribosomal protein S6 kinase B1
Structure information
PDB:3WE4
PubMed:25078151
Release date:2014-08-06
Resolution:2 Å
 
Kinase:RPS6KB1 (p70S6K)
Family:RSK
Group:AGC
Species:HUMAN
 
Quality Score:8
Missing Residues:0
Missing Atoms:0
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (2.8Å)
 
 
ASP rotation (xDFG.81) :339°
PHE rotation (xDFG.82) :23°
Activation loop position:-3.4Å
αC-helix position:17.7Å
 
G-rich loop angle:62.5°
G-rich loop distance:20Å
G-rich loop rotation:55.8°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I3
H-bond ligand
H-bond protein
I4
H-bond protein
I5
H-bond protein
I7
H-bond ligand
I10
H-bond ligand
H-bond protein
Binding pocket sequence
UniprotRVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC
Structure:RVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC


Modified residues
Residue 252 (not in pocket)
Phosphorylated threonine
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 5FI
Ligand Name: 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole

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  • LABELS
  • KLIFS residue #
  • Amino Acid
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  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
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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
95
2 V
96
3 L
97
4 G
98
5 K
99
6 G
100
7 G
101
8 Y
102
9 G
103
10 K
104
11 V
105
12 F
106
13 Q
107
14 F
120
15 A
121
16 M
122
17 K
123
18 V
124
19 L
125
20 H
139
αC b.l IV
21 T
140
22 K
141
23 A
142
24 E
143
25 R
144
26 N
145
27 I
146
28 L
147
29 E
148
30 E
149
31 V
150
32 K
151
33 P
153
34 F
154
35 I
155
36 V
156
37 D
157
38 L
158
39 I
159
40 Y
160
IV V GK hinge linker αD αE
41 A
161
42 Y
169
43 L
170
44 I
171
45 L
172
46 E
173
47 Y
174
48 L
175
49 S
176
50 G
177
51 G
178
52 E
179
53 L
180
54 F
181
55 M
182
56 Q
183
57 L
184
58 E
185
59 R
186
60 H
208
αE VI c.l VII VIII x
61 L
209
62 H
210
63 Q
211
64 K
212
65 G
213
66 I
214
67 I
215
68 Y
216
69 R
217
70 D
218
71 L
219
72 K
220
73 P
221
74 E
222
75 N
223
76 I
224
77 M
225
78 L
226
79 L
234
80 T
235
DFG a.l
81 D
236
82 F
237
83 G
238
84 L
239
85 C
240

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Binding affinities
ChEMBL ID:CHEMBL2134202
Bioaffinities: 2 records for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensRibosomal protein S6 kinase 16.86.86.8pIC501
Homo sapiensRibosomal protein S6 kinase 17.77.77.7pKi1