4OTP - chain A | Serine/threonine-protein kinase RIO1
Structure information
PDB:4OTP
PubMed:24948609
Release date:2014-07-02
Resolution:2.7 Å
 
Kinase:RIOK1
Family:RIO
Group:Atypical
Species:HUMAN
 
Quality Score:9.2
Missing Residues:0
Missing Atoms:4
DFG conformation:in
αC-helix conformation:in
Salt bridge KIII.17 and EαC.24:Yes (3Å)
 
 
ASP rotation (xDFG.81) :327°
PHE rotation (xDFG.82) :344°
Activation loop position:-3.5Å
αC-helix position:16.5Å
 
G-rich loop angle:52.5°
G-rich loop distance:16.8Å
G-rich loop rotation:20.1°
2D & 3D views

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


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: ADP
Ligand Name: ADENOSINE-5'-DIPHOSPHATE

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  • LABELS
  • KLIFS residue #
  • Amino Acid
  • None
  • 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 G
184
2 C
185
3 I
186
4 S
187
5 T
188
6 G
189
7 K
190
8 E
191
9 A
192
10 N
193
11 V
194
12 Y
195
13 H
196
14 R
205
15 A
206
16 I
207
17 K
208
18 I
209
19 Y
210
20 W
246
αC b.l IV
21 A
247
22 E
248
23 K
249
24 E
250
25 M
251
26 R
252
27 N
253
28 L
254
29 I
255
30 R
256
31 L
257
32 N
258
33 I
262
34 P
263
35 C
264
36 P
265
37 E
266
38 P
267
39 I
268
40 M
269
IV V GK hinge linker αD αE
41 L
270
42 V
274
43 L
275
44 V
276
45 M
277
46 S
278
47 F
279
48 I
280
49 G
281
50 A
287
51 P
288
52 L
289
53 L
290
54 K
291
55 N
292
56 V
293
57 Q
294
58 L
295
59 S
296
60 M
314
αE VI c.l VII VIII x
61 Y
315
62 Q
316
63 D
317
64 A
318
65 R
319
66 L
320
67 V
321
68 H
322
69 A
323
70 D
324
71 L
325
72 S
326
73 E
327
74 F
328
75 N
329
76 M
330
77 L
331
78 Y
332
79 I
339
80 I
340
DFG a.l
81 X
341
82 V
342
83 S
343
84 Q
344
85 S
345

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Binding affinities
ChEMBL ID:CHEMBL14830
Bioaffinities: 2 records for 1 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensMitogen-activated protein kinase kinase kinase 74.24.25.4pKd2