4NW6 - chain A (model B) | Ribosomal protein S6 kinase A3
Structure information
PDB:4NW6
PubMed:24534486
Release date:2014-02-19
Resolution:1.74 Å
 
Kinase:RPS6KA3 (RSK2)
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) :
PHE rotation (xDFG.82) :13°
Activation loop position:-4.5Å
αC-helix position:17.5Å
 
G-rich loop angle:49.9°
G-rich loop distance:14.8Å
G-rich loop rotation:90.7°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I2
H-bond protein
I11
H-bond protein
Binding pocket sequence
UniprotKVLGQGSFGKVFLYAMKVLRTKMERDILVEVNPFIVKLHYAYLILDFLRGGDLFTRLSKHLHSLGIIYRDLKPENILLLTDFGLS
Structure:KVLGQGSFGKVFLYAMKVLRTKMERDILVEVNPFIVKLHYAYLILDFLRGGDLFTRLSKHLHSLGIIYRDLKPENILLLTDFGLS


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 2NS
Ligand Name: 7-(1H-benzimidazol-7-yl)-N-(3,4,5-trimethoxyphenyl)-1,3-benzoxazol-2-amine

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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 K
72
2 V
73
3 L
74
4 G
75
5 Q
76
6 G
77
7 S
78
8 F
79
9 G
80
10 K
81
11 V
82
12 F
83
13 L
84
14 Y
97
15 A
98
16 M
99
17 K
100
18 V
101
19 L
102
20 R
114
αC b.l IV
21 T
115
22 K
116
23 M
117
24 E
118
25 R
119
26 D
120
27 I
121
28 L
122
29 V
123
30 E
124
31 V
125
32 N
126
33 P
128
34 F
129
35 I
130
36 V
131
37 K
132
38 L
133
39 H
134
40 Y
135
IV V GK hinge linker αD αE
41 A
136
42 Y
144
43 L
145
44 I
146
45 L
147
46 D
148
47 F
149
48 L
150
49 R
151
50 G
152
51 G
153
52 D
154
53 L
155
54 F
156
55 T
157
56 R
158
57 L
159
58 S
160
59 K
161
60 H
183
αE VI c.l VII VIII x
61 L
184
62 H
185
63 S
186
64 L
187
65 G
188
66 I
189
67 I
190
68 Y
191
69 R
192
70 D
193
71 L
194
72 K
195
73 P
196
74 E
197
75 N
198
76 I
199
77 L
200
78 L
201
79 L
209
80 T
210
DFG a.l
81 D
211
82 F
212
83 G
213
84 L
214
85 S
215

Interaction pattern search
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Binding affinities
ChEMBL ID:CHEMBL3298194
Bioaffinities: 7 records for 4 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensRibosomal protein S6 kinase alpha 28.48.48.4pIC502
Mus musculusRibosomal protein S6 kinase alpha-26.16.16.1pIC502
Homo sapiensSerine/threonine-protein kinase Aurora-A6.26.26.2pIC501
Homo sapiensTyrosine-protein kinase JAK26.36.36.3pIC502