4L45 - chain A | Ribosomal protein S6 kinase B1
Structure information
PDB:4L45
PubMed:23731517
Release date:2013-07-24
Resolution:2.9 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) :355°
PHE rotation (xDFG.82) :17°
Activation loop position:-3.1Å
αC-helix position:17.7Å
 
G-rich loop angle:61.6°
G-rich loop distance:19.4Å
G-rich loop rotation:50.1°
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
UniprotRVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC
Structure:RVLGKGGYGKVFQFAMKVLHTKAERNILEEVKPFIVDLIYAYLILEYLSGGELFMQLERHLHQKGIIYRDLKPENIMLLTDFGLC


Modified residues
No modified residues identified.
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
  • None
  • COLORS
  • Interaction types
  • KLIFS (all res.)
  • KLIFS (interacting res.)
  • None
  • OTHER
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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
72
2 V
73
3 L
74
4 G
75
5 K
76
6 G
77
7 G
78
8 Y
79
9 G
80
10 K
81
11 V
82
12 F
83
13 Q
84
14 F
97
15 A
98
16 M
99
17 K
100
18 V
101
19 L
102
20 H
116
αC b.l IV
21 T
117
22 K
118
23 A
119
24 E
120
25 R
121
26 N
122
27 I
123
28 L
124
29 E
125
30 E
126
31 V
127
32 K
128
33 P
130
34 F
131
35 I
132
36 V
133
37 D
134
38 L
135
39 I
136
40 Y
137
IV V GK hinge linker αD αE
41 A
138
42 Y
146
43 L
147
44 I
148
45 L
149
46 E
150
47 Y
151
48 L
152
49 S
153
50 G
154
51 G
155
52 E
156
53 L
157
54 F
158
55 M
159
56 Q
160
57 L
161
58 E
162
59 R
163
60 H
185
αE VI c.l VII VIII x
61 L
186
62 H
187
63 Q
188
64 K
189
65 G
190
66 I
191
67 I
192
68 Y
193
69 R
194
70 D
195
71 L
196
72 K
197
73 P
198
74 E
199
75 N
200
76 I
201
77 M
202
78 L
203
79 L
211
80 T
212
DFG a.l
81 D
213
82 F
214
83 G
215
84 L
216
85 C
217

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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