3V5W - chain A (model B) | Adrenergic, beta, receptor kinase 1
Structure information
PDB:3V5W
PubMed:22882301
Release date:2012-09-26
Resolution:2.07 Å
 
Kinase:GRK2 (BARK1)
Family:GRK
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 (2.9Å)
 
 
ASP rotation (xDFG.81) :353°
PHE rotation (xDFG.82) :344°
Activation loop position:-3.6Å
αC-helix position:17.6Å
 
G-rich loop angle:58.8°
G-rich loop distance:17.5Å
G-rich loop rotation:69.3°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
The following waters were found in the defined clusters:
I4
H-bond protein
I5
H-bond protein
I7
H-bond protein
Binding pocket sequence
UniprotRIIGRGGFGEVYGYAMKCLLALNERIMLSLVSPFIVCMSYASFILDLMNGGDLHYHLSQHMHNRFVVYRDLKPANILLISDLGLA
Structure:RIIGRGGFGEVYGYAMKCLLALNERIMLSLVSPFIVCMSYASFILDLMNGGDLHYHLSQHMHNRFVVYRDLKPANILLISDLGLA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: 8PR
Ligand Name: Paroxetine

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  • KLIFS residue #
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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
195
2 I
196
3 I
197
4 G
198
5 R
199
6 G
200
7 G
201
8 F
202
9 G
203
10 E
204
11 V
205
12 Y
206
13 G
207
14 Y
217
15 A
218
16 M
219
17 K
220
18 C
221
19 L
222
20 L
235
αC b.l IV
21 A
236
22 L
237
23 N
238
24 E
239
25 R
240
26 I
241
27 M
242
28 L
243
29 S
244
30 L
245
31 V
246
32 S
247
33 P
252
34 F
253
35 I
254
36 V
255
37 C
256
38 M
257
39 S
258
40 Y
259
IV V GK hinge linker αD αE
41 A
260
42 S
268
43 F
269
44 I
270
45 L
271
46 D
272
47 L
273
48 M
274
49 N
275
50 G
276
51 G
277
52 D
278
53 L
279
54 H
280
55 Y
281
56 H
282
57 L
283
58 S
284
59 Q
285
60 H
307
αE VI c.l VII VIII x
61 M
308
62 H
309
63 N
310
64 R
311
65 F
312
66 V
313
67 V
314
68 Y
315
69 R
316
70 D
317
71 L
318
72 K
319
73 P
320
74 A
321
75 N
322
76 I
323
77 L
324
78 L
325
79 I
333
80 S
334
DFG a.l
81 D
335
82 L
336
83 G
337
84 L
338
85 A
339

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Binding affinities
ChEMBL ID:CHEMBL490
Bioaffinities: 4 records for 2 kinase(s)

Species Kinase (ChEMBL naming) Median Min Max Type Records
Bos taurusBeta-adrenergic receptor kinase 15.95.95.9pIC501
Homo sapiensG-protein coupled receptor kinase 25.95.96pIC503