5MYV - chain D (model B) | SRSF protein kinase 2
Structure information
PDB:5MYV
PubMed:28135068
Release date:2017-05-10
Resolution:2.9 Å
 
Kinase:SRPK2
Family:SRPK
Group:CMGC
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 (3.1Å)
 
 
ASP rotation (xDFG.81) :341°
PHE rotation (xDFG.82) :
Activation loop position:-3.3Å
αC-helix position:17.9Å
 
G-rich loop angle:54.1°
G-rich loop distance:17.2Å
G-rich loop rotation:59.7°
Other models from this PDB:
2D & 3D views

The orthosteric binding pocket
Binding pocket waters
No waters were found in the defined clusters
Binding pocket sequence
UniprotRKLGWGHFSTVWLVAMKVVTALDEIKLLKCVRDMVVQLIDDCMVFEVLG-HHLLKWIIKLHSKCKIIHTDIKPENILMIADLGNA
Structure:RKLGWGHFSTVWLVAMKVVTALDEIKLLKCVRDMVVQLIDDCMVFEVLG_HHLLKWIIKLHSKCKIIHTDIKPENILMIADLGNA


Modified residues
No modified residues identified.
Orthosteric ligand
2D structure of the orthosteric ligand
Ligand HET-code: W4A
Ligand Name: 5-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-(trifluoromethyl)phenyl]furan-2-carboxamide

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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 R
96
2 K
97
3 L
98
4 G
99
5 W
100
6 G
101
7 H
102
8 F
103
9 S
104
10 T
105
11 V
106
12 W
107
13 L
108
14 V
118
15 A
119
16 M
120
17 K
121
18 V
122
19 V
123
20 T
132
αC b.l IV
21 A
133
22 L
134
23 D
135
24 E
136
25 I
137
26 K
138
27 L
139
28 L
140
29 K
141
30 C
142
31 V
143
32 R
144
33 D
154
34 M
155
35 V
156
36 V
157
37 Q
158
38 L
159
39 I
160
40 D
161
IV V GK hinge linker αD αE
41 D
162
42 C
174
43 M
175
44 V
176
45 F
177
46 E
178
47 V
179
48 L
180
49 G
181
50 _
_
51 H
182
52 H
183
53 L
184
54 L
185
55 K
186
56 W
187
57 I
188
58 I
189
59 K
190
60 L
215
αE VI c.l VII VIII x
61 H
216
62 S
217
63 K
218
64 C
219
65 K
220
66 I
221
67 I
222
68 H
223
69 T
224
70 D
225
71 I
226
72 K
227
73 P
228
74 E
229
75 N
230
76 I
231
77 L
232
78 M
233
79 I
539
80 A
540
DFG a.l
81 D
541
82 L
542
83 G
543
84 N
544
85 A
545

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Binding affinities
Ligand not found in ChEMBL.